Variant report

Variant	rs6484639
Chromosome Location	chr11:33082193-33082194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:33060257..33064189-chr11:33080960..33084612,4	K562	blood:
2	chr11:33059371..33062523-chr11:33080463..33084324,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176148	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1033716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10430851	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10430950	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10767986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032141	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1407044	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964136	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2273539	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273544	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3740801	0.92[ASN][1000 genomes]
rs3758743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4261257	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4275605	0.89[AFR][1000 genomes]
rs4310578	0.92[ASN][1000 genomes]
rs4382878	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4439489	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4442529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]
rs4445605	0.84[ASN][1000 genomes]
rs4561187	1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4755486	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4755487	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6484638	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6484643	0.89[ASN][1000 genomes]
rs7108667	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7114010	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7125132	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7125873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129799	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7130318	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951757	0.83[AMR][1000 genomes];0.90[EUR][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	esv2753743	chr11:32796124-33084924	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv1040484	chr11:32951066-33093204	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6484639	LOC283267	Cis_1M	lymphoblastoid	RTeQTL
rs6484639	TCP11L1	Cis_1M	lymphoblastoid	RTeQTL
rs6484639	TCP11L1	cis	multi-tissue	Pritchard
rs6484639	TCP11L1	cis	Artery Tibial	GTEx
rs6484639	PIGCP1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:33062000-33093600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:33062200-33085400	Weak transcription	Psoas Muscle	Psoas
3	chr11:33062600-33084800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr11:33062600-33094200	Weak transcription	Fetal Heart	heart
5	chr11:33062800-33084600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr11:33062800-33084800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr11:33062800-33107400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:33063600-33084800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr11:33067800-33085800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:33072600-33098800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr11:33074400-33083000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:33074400-33085400	Strong transcription	Fetal Muscle Leg	muscle
13	chr11:33075000-33082200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:33075000-33130200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:33075600-33083600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr11:33075800-33082200	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr11:33076000-33082200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr11:33076000-33129600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:33076200-33082400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:33076200-33083400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr11:33076200-33084800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:33076400-33085800	Strong transcription	Left Ventricle	heart
23	chr11:33076600-33104600	Strong transcription	Fetal Brain Female	brain
24	chr11:33077200-33082200	Weak transcription	HepG2	liver
25	chr11:33078000-33085600	Strong transcription	Placenta	Placenta
26	chr11:33078200-33084600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:33078200-33084800	Strong transcription	Brain Anterior Caudate	brain
28	chr11:33078200-33109000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:33078400-33082200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:33078400-33082400	Strong transcription	NH-A	brain
31	chr11:33078400-33083200	Strong transcription	Primary B cells from cord blood	blood
32	chr11:33078400-33083200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr11:33078400-33083600	Strong transcription	Primary T cells from cord blood	blood
34	chr11:33078400-33084400	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr11:33078400-33084400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr11:33078400-33084600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr11:33078400-33085200	Strong transcription	Adipose Nuclei	Adipose
38	chr11:33078400-33086200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr11:33078600-33082200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr11:33078600-33082200	Strong transcription	Osteobl	bone
41	chr11:33078600-33109600	Strong transcription	Dnd41	blood
42	chr11:33078800-33082200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr11:33078800-33084400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr11:33079000-33082200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:33079000-33082400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:33079000-33085200	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr11:33079000-33085200	Weak transcription	K562	blood
48	chr11:33079000-33085600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr11:33079000-33085800	Strong transcription	Fetal Stomach	stomach
50	chr11:33079200-33082200	Strong transcription	NHDF-Ad	bronchial

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