Variant report

Variant	rs12796411
Chromosome Location	chr11:33111581-33111582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:33111512-33111655	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr11:33111440-33111590	HFF	foreskin:	n/a	n/a
3	CTCF	chr11:33111500-33111650	HAc	cerebellar:	n/a	n/a
4	CTCF	chr11:33111500-33111650	AoAF	blood vessel:	n/a	n/a
5	CTCF	chr11:33111440-33111590	GM12878	blood:	n/a	n/a
6	CTCF	chr11:33111500-33111650	HCFaa	heart:	n/a	n/a
7	CTCF	chr11:33111500-33111650	HMEC	breast:	n/a	n/a
8	POLR2A	chr11:33111535-33111636	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr11:33111480-33111630	HBMEC	blood vessel:	n/a	n/a
10	CTCF	chr11:33111540-33111690	MCF-7	breast:	n/a	n/a
11	CTCF	chr11:33111520-33111670	GM12871	blood:	n/a	n/a
12	CTCF	chr11:33111500-33111650	Caco-2	colon:	n/a	n/a
13	CTCF	chr11:33111520-33111670	HBMEC	blood vessel:	n/a	n/a
14	CTCF	chr11:33111540-33111690	HPAF	blood vessel:	n/a	n/a
15	CTCF	chr11:33111480-33111630	GM12869	blood:	n/a	n/a
16	CTCF	chr11:33111500-33111650	MCF-7	breast:	n/a	n/a
17	CTCF	chr11:33111460-33111610	AG09309	skin:	n/a	n/a
18	POLR2A	chr11:33110580-33111604	A549	lung:	n/a	n/a
19	CTCF	chr11:33111520-33111670	Caco-2	colon:	n/a	n/a
20	CTCF	chr11:33111480-33111630	GM12872	blood:	n/a	n/a
21	RAD21	chr11:33111458-33111718	IMR90	lung:	n/a	n/a
22	ZNF143	chr11:33111503-33111595	GM12878	blood:	n/a	n/a
23	CTCF	chr11:33111520-33111670	HEEpiC	esophagus:	n/a	n/a
24	CTCF	chr11:33111560-33111710	AG09319	gingival:	n/a	n/a
25	POLR2A	chr11:33111462-33114028	K562	blood:	n/a	n/a
26	CTCF	chr11:33111540-33111690	HMEC	breast:	n/a	n/a
27	CTCF	chr11:33111540-33111690	GM12870	blood:	n/a	n/a
28	CTCF	chr11:33111520-33111670	AG10803	skin:	n/a	n/a
29	CTCF	chr11:33111486-33111594	MCF-7	breast:	n/a	n/a
30	CTCF	chr11:33111500-33111650	HPAF	blood vessel:	n/a	n/a
31	CTCF	chr11:33111500-33111650	NHDF-neo	bronchial:	n/a	n/a
32	CTCF	chr11:33111520-33111670	HEK293	kidney:	n/a	n/a
33	CTCF	chr11:33111439-33111677	GM12878	blood:	n/a	n/a
34	CTCF	chr11:33111480-33111630	NHDF-neo	bronchial:	n/a	n/a
35	BATF	chr11:33111397-33111588	GM12878	blood:	n/a	chr11:33111512-33111523
36	CTCF	chr11:33111520-33111670	HCM	heart:	n/a	n/a
37	CTCF	chr11:33111560-33111710	GM12864	blood:	n/a	n/a
38	CTCF	chr11:33111480-33111630	AG09319	gingival:	n/a	n/a
39	CTCF	chr11:33111439-33111645	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr11:33111439-33111754	IMR90	lung:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:33110539..33112969-chr11:33181775..33184270,2	MCF-7	breast:
2	chr11:33107993..33109639-chr11:33110999..33113012,2	K562	blood:

No data

Variant related genes	Relation type
CSTF3	TF binding region
ENSG00000176102	Chromatin interaction
ENSG00000247151	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11601995	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11604958	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11605353	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12789131	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12789704	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12791322	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12799348	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12800094	0.81[AFR][1000 genomes]
rs12801004	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12804226	0.84[ASN][1000 genomes]
rs12807007	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3117655	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3117656	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34517146	0.83[ASN][1000 genomes]
rs3758741	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs419003	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs432219	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4756112	0.83[ASN][1000 genomes]
rs59425655	0.82[ASN][1000 genomes]
rs7103953	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7947938	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762904	chr11:32969258-33586535	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1041149	chr11:32981164-33496670	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1053823	chr11:32981164-33533356	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv897194	chr11:32993887-33471804	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1040572	chr11:33008191-33518964	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv540989	chr11:33008191-33518964	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1042860	chr11:33008191-33562490	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv540990	chr11:33008191-33562490	Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
9	nsv533840	chr11:33008192-33595324	Bivalent Enhancer Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	nsv1051521	chr11:33008435-33239765	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv540991	chr11:33008435-33239765	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv1044478	chr11:33008435-33656273	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	nsv897195	chr11:33012493-33559186	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
14	nsv1053344	chr11:33028973-33499346	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
15	nsv1046243	chr11:33043155-33439216	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
16	nsv540992	chr11:33043155-33439216	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
17	nsv1050944	chr11:33043155-33656273	Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
18	nsv540993	chr11:33043155-33656273	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
19	nsv529212	chr11:33053073-33641691	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
20	nsv869418	chr11:33053073-33662479	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
21	nsv467786	chr11:33065394-33476703	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
22	nsv553994	chr11:33065394-33476703	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
23	nsv521130	chr11:33068389-33602913	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
24	nsv1049756	chr11:33075082-33496670	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
25	nsv1053959	chr11:33075082-33565833	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
26	nsv540994	chr11:33075082-33565833	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
27	nsv975378	chr11:33105191-33112610	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
28	nsv897196	chr11:33106616-33152074	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12796411	TCP11L1	Cis_1M	lymphoblastoid	RTeQTL
rs12796411	TCP11L1	cis	Muscle Skeletal	GTEx
rs12796411	PIGCP1	cis	Muscle Skeletal	GTEx
rs12796411	LOC283267	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:33075000-33130200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:33076000-33129600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:33085200-33112000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:33085600-33122000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:33086200-33122000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:33086400-33127400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:33086600-33119400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr11:33087200-33113600	Strong transcription	Placenta	Placenta
9	chr11:33087200-33129400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:33087800-33111800	Strong transcription	A549	lung
11	chr11:33087800-33138000	Weak transcription	Stomach Mucosa	stomach
12	chr11:33089400-33113600	Strong transcription	Fetal Thymus	thymus
13	chr11:33094400-33117600	Weak transcription	Fetal Kidney	kidney
14	chr11:33094400-33121400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:33094800-33119400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr11:33095000-33126800	Weak transcription	Right Ventricle	heart
17	chr11:33095200-33119600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr11:33095400-33117400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr11:33097800-33117600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr11:33097800-33117800	Weak transcription	Hela-S3	cervix
21	chr11:33098000-33121400	Weak transcription	Small Intestine	intestine
22	chr11:33098000-33122600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:33098800-33127400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:33099200-33114000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:33099200-33129400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr11:33099400-33118800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr11:33100600-33121400	Weak transcription	Aorta	Aorta
28	chr11:33100800-33122000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr11:33100800-33123800	Weak transcription	Fetal Brain Male	brain
30	chr11:33101600-33122400	Weak transcription	Esophagus	oesophagus
31	chr11:33102600-33114400	Strong transcription	HSMM	muscle
32	chr11:33103000-33111600	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:33103000-33113600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr11:33103400-33113000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:33103600-33128600	Weak transcription	Gastric	stomach
36	chr11:33103800-33113200	Strong transcription	Primary B cells from cord blood	blood
37	chr11:33104200-33128400	Weak transcription	Pancreas	Pancrea
38	chr11:33104800-33122600	Weak transcription	Spleen	Spleen
39	chr11:33104800-33133600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr11:33105000-33118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:33105400-33114400	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr11:33106200-33111600	Strong transcription	Fetal Muscle Leg	muscle
43	chr11:33106800-33119200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr11:33106800-33131600	Weak transcription	Psoas Muscle	Psoas
45	chr11:33107000-33114400	Strong transcription	Primary T cells from cord blood	blood
46	chr11:33107000-33119400	Weak transcription	Thymus	Thymus
47	chr11:33107200-33121400	Weak transcription	Lung	lung
48	chr11:33107200-33124600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:33107400-33111800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr11:33107600-33111800	Weak transcription	Duodenum Mucosa	Duodenum

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