Variant report

Variant	rs13219624
Chromosome Location	chr6:34861799-34861800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34860202..34861936-chr6:34863788..34865891,2	MCF-7	breast:
2	chr6:34855616..34859165-chr6:34859193..34863174,8	MCF-7	breast:
3	chr6:34844007..34846659-chr6:34861219..34864126,3	K562	blood:

Variant related genes	Relation type
ENSG00000064995	Chromatin interaction
ENSG00000064999	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1051115	0.82[YRI][hapmap]
rs10947536	0.94[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap]
rs12212217	0.86[CHB][hapmap];0.96[YRI][hapmap]
rs13191009	0.82[AFR][1000 genomes]
rs13218101	0.99[ASN][1000 genomes]
rs1535001	0.81[GIH][hapmap]
rs1555107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16896390	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1737727	0.94[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2140418	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs2177381	0.94[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap]
rs2273006	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2293242	0.94[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs2473613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2473615	0.82[GIH][hapmap]
rs2504162	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2985	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3734262	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3800451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646933	0.82[YRI][hapmap]
rs4646940	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646944	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4646949	0.82[GIH][hapmap]
rs6457797	0.85[LWK][hapmap];0.82[YRI][hapmap]
rs6905468	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6907619	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6918183	0.93[ASN][1000 genomes]
rs6918872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6932857	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6941065	0.89[LWK][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];0.80[YRI][hapmap]
rs7739385	0.82[YRI][hapmap]
rs7739991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7753949	0.85[GIH][hapmap]
rs7757211	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs847846	0.81[GIH][hapmap]
rs847847	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs847848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9296139	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368834	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9368836	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9394252	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS 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	49 gene(s)	inside rSNPs	diseases
4	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1020710	chr6:34607214-34890143	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv870010	chr6:34713359-34880048	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv1025374	chr6:34723723-34887316	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv462905	chr6:34728253-34886436	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv602906	chr6:34728253-34886436	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv1015792	chr6:34741917-34887316	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv1021733	chr6:34751052-34887316	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv1026121	chr6:34786887-34961360	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
14	nsv885797	chr6:34791027-34980601	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
15	nsv1033135	chr6:34802652-34957093	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
16	nsv508402	chr6:34840961-34951288	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13219624	TAF11	cis	lymphoblastoid	seeQTL
rs13219624	PRDM7	trans	multi-tissue	Pritchard

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34857800-34869200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:34858000-34877600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:34858200-34870800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:34858200-34873400	Weak transcription	Esophagus	oesophagus
5	chr6:34858400-34877400	Weak transcription	Aorta	Aorta
6	chr6:34858600-34864800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:34858600-34869400	Weak transcription	NHDF-Ad	bronchial
8	chr6:34858600-34879200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:34858800-34880200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:34859000-34862200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:34859000-34862600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:34859000-34862600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:34859000-34863000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:34859000-34863000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:34859000-34863000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:34859000-34863000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:34859000-34865200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:34859000-34868600	Weak transcription	Osteobl	bone
19	chr6:34859000-34869000	Weak transcription	Fetal Lung	lung
20	chr6:34859000-34869400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:34859000-34869400	Weak transcription	Lung	lung
22	chr6:34859000-34871600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:34859000-34874000	Weak transcription	Brain Anterior Caudate	brain
24	chr6:34859000-34875200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:34859000-34879600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr6:34859200-34864400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:34859200-34864600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr6:34859200-34865000	Weak transcription	HSMMtube	muscle
29	chr6:34859200-34865600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr6:34859200-34868400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:34859200-34874800	Weak transcription	K562	blood
32	chr6:34859200-34876800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr6:34859200-34879000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:34859200-34882400	Weak transcription	Fetal Stomach	stomach
35	chr6:34859200-34884600	Weak transcription	Fetal Muscle Leg	muscle
36	chr6:34859200-34884800	Weak transcription	Right Ventricle	heart
37	chr6:34859200-34890800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr6:34859400-34861800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:34859400-34862200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:34859400-34873400	Weak transcription	Stomach Mucosa	stomach
41	chr6:34859400-34879400	Weak transcription	Primary T cells from cord blood	blood
42	chr6:34859400-34880200	Weak transcription	Primary B cells from cord blood	blood
43	chr6:34859600-34872800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:34859600-34873800	Weak transcription	Ovary	ovary
45	chr6:34860000-34861800	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr6:34860000-34863000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:34860000-34864800	Weak transcription	Adipose Nuclei	Adipose
48	chr6:34860000-34864800	Weak transcription	Left Ventricle	heart
49	chr6:34860000-34865600	Weak transcription	Right Atrium	heart
50	chr6:34860000-34868200	Weak transcription	Monocytes-CD14+_RO01746	blood

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