Variant report

Variant	rs6999808
Chromosome Location	chr8:120804892-120804893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:120804864-120804994	K562	blood:	n/a	n/a
2	POLR2A	chr8:120804775-120806422	K562	blood:	n/a	n/a
3	POLR2A	chr8:120804770-120805059	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr8:120804862-120805027	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
TAF2	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10087974	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10088205	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10088741	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10089416	0.81[YRI][hapmap]
rs10108101	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1055131	0.89[YRI][hapmap]
rs1055133	0.90[YRI][hapmap]
rs11785572	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11985347	0.88[EUR][1000 genomes]
rs11996390	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11998531	0.89[EUR][1000 genomes]
rs12156318	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1355174	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893214	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16893240	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16893243	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16893252	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17818097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17818440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17818446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17818842	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2063283	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2063284	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28394804	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28490296	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28551477	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871595	0.90[YRI][hapmap]
rs4871629	0.90[YRI][hapmap]
rs4871648	0.90[YRI][hapmap]
rs56180159	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56281801	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56366115	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60145621	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60917006	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61438417	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62526598	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62526601	0.86[ASN][1000 genomes]
rs62526606	0.86[ASN][1000 genomes]
rs6469845	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6469846	0.89[YRI][hapmap]
rs6469856	1.00[CHB][hapmap]
rs6469858	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6981251	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6987018	1.00[CHB][hapmap]
rs6987100	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6987389	1.00[JPT][hapmap]
rs6988621	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6989559	0.90[YRI][hapmap]
rs6989803	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6994085	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6995594	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7002440	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7002501	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7003687	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7007320	1.00[CHB][hapmap]
rs7007970	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7012857	0.89[YRI][hapmap]
rs7017010	0.90[YRI][hapmap]
rs7813113	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7813680	0.89[YRI][hapmap]
rs7815122	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7815389	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7827811	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7828086	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7831639	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7831973	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7833490	0.90[YRI][hapmap]
rs7836830	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7837894	1.00[JPT][hapmap]
rs7838465	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7843080	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7843579	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9297606	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953614	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs953615	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9650078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534028	chr8:120348940-120906079	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv949368	chr8:120568034-121019872	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1021071	chr8:120589963-120968317	Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers 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	30 gene(s)	inside rSNPs	diseases
5	nsv465789	chr8:120636850-120994394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv612111	chr8:120636850-120994394	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv427826	chr8:120642181-120953395	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	esv3481251	chr8:120800778-120823850	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3481253	chr8:120800792-120823847	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6999808	DSCC1	cis	Artery Tibial	GTEx
rs6999808	DSCC1	cis	Skin Sun Exposed Lower leg	GTEx
rs6999808	TAF2	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120742600-120812800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr8:120744000-120814600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:120744400-120824400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr8:120767200-120807400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr8:120781000-120807000	Weak transcription	Brain Angular Gyrus	brain
6	chr8:120781000-120813800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr8:120781200-120807000	Weak transcription	Colon Smooth Muscle	Colon
8	chr8:120781200-120807800	Weak transcription	NHLF	lung
9	chr8:120781200-120812800	Weak transcription	Colonic Mucosa	Colon
10	chr8:120781200-120829400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:120781400-120805000	Weak transcription	Gastric	stomach
12	chr8:120781400-120812800	Weak transcription	Right Ventricle	heart
13	chr8:120781400-120813800	Weak transcription	Aorta	Aorta
14	chr8:120781600-120812800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr8:120781600-120844200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr8:120785200-120812000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr8:120785200-120812600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr8:120785600-120810600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr8:120785800-120808800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr8:120785800-120810400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr8:120786600-120810000	Strong transcription	Fetal Thymus	thymus
22	chr8:120788800-120805800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:120791000-120833200	Weak transcription	Fetal Heart	heart
24	chr8:120791400-120807200	Weak transcription	Fetal Brain Male	brain
25	chr8:120792400-120812600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr8:120792800-120806800	Weak transcription	Fetal Kidney	kidney
27	chr8:120793400-120814200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr8:120794800-120810800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr8:120795800-120812800	Weak transcription	HSMMtube	muscle
30	chr8:120796600-120805600	Weak transcription	HMEC	breast
31	chr8:120797200-120812800	Weak transcription	Brain Germinal Matrix	brain
32	chr8:120798200-120805600	Weak transcription	GM12878-XiMat	blood
33	chr8:120798600-120811000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr8:120800200-120821800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr8:120800400-120805200	Strong transcription	Fetal Brain Female	brain
36	chr8:120800400-120805400	Strong transcription	Placenta	Placenta
37	chr8:120800400-120808200	Strong transcription	Adipose Nuclei	Adipose
38	chr8:120800400-120810000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr8:120800400-120810200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr8:120800400-120810200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr8:120800400-120810400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr8:120800400-120810800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr8:120800400-120810800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr8:120800400-120810800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr8:120800400-120812800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr8:120800600-120805200	Strong transcription	Fetal Lung	lung
47	chr8:120800600-120805400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr8:120800600-120805400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr8:120800600-120805600	Strong transcription	Liver	Liver
50	chr8:120800600-120808000	Strong transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links