Variant report

Variant	rs12790040
Chromosome Location	chr11:67037274-67037275
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:67036718-67037589	GM12892	blood:	n/a	n/a
2	POLR2A	chr11:67036748-67037365	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:67033773-67040167	NB4	blood:	n/a	n/a
4	EBF1	chr11:67036802-67037425	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:67036690-67037532	K562	blood:	n/a	n/a
6	STAT5A	chr11:67034406-67037282	GM12878	blood:	n/a	chr11:67035955-67035963
7	POLR2A	chr11:67034482-67038045	GM12892	blood:	n/a	n/a
8	PML	chr11:67037132-67038971	GM12878	blood:	n/a	chr11:67037760-67037768
9	WRNIP1	chr11:67036895-67039166	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:67036738-67038616	K562	blood:	n/a	n/a
11	POLR2A	chr11:67034324-67041514	HL-60	blood:	n/a	n/a
12	POLR2A	chr11:67033578-67041547	HL-60	blood:	n/a	n/a
13	POLR2A	chr11:67036808-67037565	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:67037197-67038282	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr11:67033515-67041155	GM12892	blood:	n/a	n/a
16	POLR2A	chr11:67034580-67038739	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:67036933-67037340	K562	blood:	n/a	n/a
18	CHD1	chr11:67036808-67037921	GM12878	blood:	n/a	n/a
19	MTA3	chr11:67036700-67038833	GM12878	blood:	n/a	n/a
20	POLR2A	chr11:67037071-67038376	SK-N-MC	brain:	n/a	n/a
21	RUNX3	chr11:67036771-67037402	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:67030856..67037366-chr11:67138319..67144892,13	MCF-7	breast:
2	chr11:67035184..67037391-chr11:67122258..67124075,2	MCF-7	breast:
3	chr11:67033933..67038277-chr11:67140224..67143646,5	MCF-7	breast:
4	chr11:67036910..67037602-chr6:33267260..33267803,2	NB4	blood:

No data

Variant related genes	Relation type
ADRBK1	TF binding region
ENSG00000256514	Chromatin interaction
ENSG00000175505	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10896166	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11819783	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12288048	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12788405	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12791853	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1419861	0.84[ASN][1000 genomes]
rs1638569	0.81[ASN][1000 genomes]
rs17878756	0.81[ASN][1000 genomes]
rs17883741	0.81[ASN][1000 genomes]
rs1790731	0.84[ASN][1000 genomes]
rs1790735	0.84[ASN][1000 genomes]
rs1790737	0.81[ASN][1000 genomes]
rs1790738	0.81[ASN][1000 genomes]
rs1790739	0.81[ASN][1000 genomes]
rs1790762	0.84[ASN][1000 genomes]
rs1894112	0.84[ASN][1000 genomes]
rs1944096	0.84[ASN][1000 genomes]
rs2286619	0.81[ASN][1000 genomes]
rs2298815	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2429459	0.84[ASN][1000 genomes]
rs2429463	0.84[ASN][1000 genomes]
rs2511057	0.84[ASN][1000 genomes]
rs2514257	0.84[ASN][1000 genomes]
rs2532605	0.84[ASN][1000 genomes]
rs35247976	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35821109	0.81[ASN][1000 genomes]
rs35876769	0.81[ASN][1000 genomes]
rs3737460	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4244822	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59551907	0.87[AFR][1000 genomes]
rs61734600	0.81[ASN][1000 genomes]
rs66466718	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs71457775	0.81[ASN][1000 genomes]
rs7394531	0.81[ASN][1000 genomes]
rs7934433	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs867193	0.81[ASN][1000 genomes]
rs9734588	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv933183	chr11:67008447-67160993	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv897796	chr11:67021518-67186000	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv897797	chr11:67023040-67293234	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers 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 miRNA target site	206 gene(s)	inside rSNPs	diseases
5	nsv897798	chr11:67024534-67065858	Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv897799	chr11:67024534-67072623	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv897800	chr11:67024534-67086298	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
9	nsv468603	chr11:67033076-67164495	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
10	nsv555253	chr11:67033076-67164495	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
11	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67034400-67039200	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr11:67034400-67041400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr11:67034600-67039400	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr11:67034600-67040800	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr11:67034600-67041400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
6	chr11:67034800-67037800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:67034800-67038200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:67034800-67039000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr11:67034800-67039800	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
10	chr11:67034800-67041000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:67035000-67037400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr11:67035000-67040400	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
13	chr11:67035000-67040400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:67035000-67040400	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
15	chr11:67035000-67040400	Transcr. at gene 5' and 3'	Thymus	Thymus
16	chr11:67035000-67040800	Weak transcription	Ovary	ovary
17	chr11:67035200-67037400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
18	chr11:67035200-67037600	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:67035200-67037600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
20	chr11:67035200-67037800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
21	chr11:67035200-67039400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:67035200-67039600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr11:67035200-67039600	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
24	chr11:67035200-67039800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
25	chr11:67035200-67040400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
26	chr11:67035400-67037400	Enhancers	Fetal Brain Male	brain
27	chr11:67035400-67037600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:67035400-67037600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
29	chr11:67035400-67038600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:67035400-67040800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr11:67035400-67044400	Weak transcription	A549	lung
32	chr11:67035600-67037400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:67035600-67037600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
34	chr11:67035600-67037600	Enhancers	HUVEC	blood vessel
35	chr11:67035600-67040000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr11:67035600-67041200	Genic enhancers	Gastric	stomach
37	chr11:67035600-67041400	Enhancers	Fetal Heart	heart
38	chr11:67035600-67041600	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr11:67035600-67046400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr11:67035800-67037400	Enhancers	Brain Substantia Nigra	brain
41	chr11:67035800-67037400	Genic enhancers	NHLF	lung
42	chr11:67035800-67037600	Genic enhancers	Placenta	Placenta
43	chr11:67035800-67038400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr11:67035800-67038400	Genic enhancers	HepG2	liver
45	chr11:67035800-67038800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
46	chr11:67035800-67044600	Enhancers	Left Ventricle	heart
47	chr11:67036000-67037400	Genic enhancers	Fetal Intestine Large	intestine
48	chr11:67036000-67040400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr11:67036000-67041000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:67036200-67037400	Enhancers	Fetal Lung	lung

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