Variant report

Variant	rs6469845
Chromosome Location	chr8:120792195-120792196
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	chr8:120790458..120793284-chr8:120795607..120798473,3	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10087974	1.00[CEU][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10088205	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10088741	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10108101	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11785572	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11985347	0.88[EUR][1000 genomes]
rs11996390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs11998531	0.89[EUR][1000 genomes]
rs12156318	0.91[EUR][1000 genomes]
rs1355174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16893214	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.82[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]
rs17818440	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17818446	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17818842	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs2063283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2063284	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28394804	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28490296	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28551477	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56180159	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56281801	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56366115	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60145621	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60917006	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61438417	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62526598	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6469842	0.87[ASW][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	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6989803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6994085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6995594	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6999808	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]
rs7002440	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7002501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7003687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7007320	1.00[CHB][hapmap]
rs7007970	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7813113	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs7815122	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs7815389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7827811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7828086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7831639	0.89[EUR][1000 genomes]
rs7831973	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7836830	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7837894	1.00[JPT][hapmap]
rs7838465	0.94[EUR][1000 genomes]
rs7843034	0.80[ASW][hapmap]
rs7843080	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7843579	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9297606	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs953614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs953615	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650078	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6469845	DSCC1	cis	Skin Sun Exposed Lower leg	GTEx
rs6469845	TAF2	cis	cerebellum	SCAN
rs6469845	DSCC1	cis	Artery Tibial	GTEx
rs6469845	DSCC1	cis	cerebellum	SCAN
rs6469845	ENPP2	cis	lymphoblastoid	seeQTL
rs6469845	DSCC1	cis	parietal	SCAN

Chromatin state (count:123 , 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	chr8:120760600-120804600	Weak transcription	Psoas Muscle	Psoas
5	chr8:120761600-120800800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr8:120767200-120807400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr8:120773600-120795000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr8:120776400-120797800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr8:120780200-120792600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr8:120780400-120801200	Weak transcription	Brain Substantia Nigra	brain
11	chr8:120781000-120807000	Weak transcription	Brain Angular Gyrus	brain
12	chr8:120781000-120813800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr8:120781200-120795000	Weak transcription	NHEK	skin
14	chr8:120781200-120795600	Weak transcription	HMEC	breast
15	chr8:120781200-120796400	Weak transcription	Pancreas	Pancrea
16	chr8:120781200-120801000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr8:120781200-120801400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr8:120781200-120804400	Weak transcription	Spleen	Spleen
19	chr8:120781200-120804600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr8:120781200-120807000	Weak transcription	Colon Smooth Muscle	Colon
21	chr8:120781200-120807800	Weak transcription	NHLF	lung
22	chr8:120781200-120812800	Weak transcription	Colonic Mucosa	Colon
23	chr8:120781200-120829400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr8:120781400-120792200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr8:120781400-120792600	Weak transcription	Left Ventricle	heart
26	chr8:120781400-120794000	Weak transcription	Ovary	ovary
27	chr8:120781400-120802800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr8:120781400-120803000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr8:120781400-120804400	Weak transcription	Esophagus	oesophagus
30	chr8:120781400-120804600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr8:120781400-120804800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr8:120781400-120805000	Weak transcription	Gastric	stomach
33	chr8:120781400-120812800	Weak transcription	Right Ventricle	heart
34	chr8:120781400-120813800	Weak transcription	Aorta	Aorta
35	chr8:120781600-120812800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr8:120781600-120844200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr8:120781800-120792200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr8:120782800-120797400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr8:120782800-120797800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr8:120782800-120799000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr8:120783800-120804400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr8:120785200-120812000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr8:120785200-120812600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr8:120785600-120797400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr8:120785600-120797400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr8:120785600-120810600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr8:120785800-120797000	Strong transcription	Liver	Liver
48	chr8:120785800-120808800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr8:120785800-120810400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr8:120786000-120797400	Strong transcription	Primary T cells fromperipheralblood	blood

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