Variant report

Variant	rs6471898
Chromosome Location	chr8:61658362-61658363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:61655145..61656697-chr8:61656892..61658859,2	K562	blood:
2	chr8:61644817..61647237-chr8:61656658..61659132,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171316	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10093135	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10103011	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10109193	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1038351	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1038352	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1038353	0.85[YRI][hapmap]
rs10448027	0.84[EUR][1000 genomes]
rs10808711	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10808712	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10808713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10957154	0.90[EUR][1000 genomes]
rs10957155	0.90[EUR][1000 genomes]
rs10957156	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10957158	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10957161	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11985638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11986742	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11988338	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11990117	0.84[ASN][1000 genomes]
rs11990495	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11991467	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11992809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11993480	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11993490	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11993896	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11995234	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11997122	0.84[ASN][1000 genomes]
rs12544305	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs12681737	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13255519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13256023	0.86[YRI][hapmap]
rs13264014	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13269752	0.86[EUR][1000 genomes]
rs13277976	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1384688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1483206	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16926407	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1905305	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1964573	0.80[EUR][1000 genomes]
rs2035456	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2035457	0.90[EUR][1000 genomes]
rs2054666	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2054667	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2128713	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2326598	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28653462	0.89[ASN][1000 genomes]
rs2875984	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4237037	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4237038	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4289855	0.84[EUR][1000 genomes]
rs4301480	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4307377	1.00[CHB][hapmap];0.80[MEX][hapmap]
rs4391471	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4392940	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4449834	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs4500113	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4526395	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4540437	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4562360	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4581092	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4737563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4737565	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4738815	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs4738818	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4738820	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4738821	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4738822	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4738824	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4738827	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4738831	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs4738832	1.00[CHB][hapmap]
rs6471894	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6471896	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6471897	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471901	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6471902	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6471903	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6471905	1.00[CHB][hapmap]
rs6982898	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6988582	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6994180	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6995557	0.90[EUR][1000 genomes]
rs6996597	0.80[EUR][1000 genomes]
rs6996775	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6997208	0.80[EUR][1000 genomes]
rs6997222	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7000766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7000957	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7002806	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7005873	1.00[CHB][hapmap]
rs7009754	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7011972	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7012450	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7016832	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7017676	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs730085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7814114	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7816126	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7816621	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7823484	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7826035	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7834076	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7834977	0.86[CHB][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7836586	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7838426	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7840098	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7842389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7842498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7843033	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7845701	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7846065	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs900502	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs9298040	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9298042	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9643371	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9650201	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active 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	74 gene(s)	inside rSNPs	diseases
2	nsv831335	chr8:61497540-61688992	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS 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	33 gene(s)	inside rSNPs	diseases
3	nsv890945	chr8:61522008-61707725	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv526196	chr8:61593569-61877623	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active 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	11 gene(s)	inside rSNPs	diseases
5	nsv1022801	chr8:61623974-61738067	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers 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	7 gene(s)	inside rSNPs	diseases
6	nsv539632	chr8:61623974-61738067	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	esv1797364	chr8:61658362-61696231	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6471898	TOX	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61638600-61664200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr8:61644200-61659200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr8:61644800-61659400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr8:61648800-61663800	Weak transcription	HUVEC	blood vessel
5	chr8:61649000-61663800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr8:61649200-61660800	Weak transcription	Small Intestine	intestine
7	chr8:61651600-61664600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr8:61652000-61663600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr8:61653200-61663400	Weak transcription	Fetal Brain Female	brain
10	chr8:61653800-61658600	Strong transcription	Primary B cells from cord blood	blood
11	chr8:61655000-61660200	Weak transcription	K562	blood
12	chr8:61655000-61664800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr8:61655000-61665400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr8:61655400-61658400	Enhancers	Brain Hippocampus Middle	brain
15	chr8:61655400-61659400	Weak transcription	NH-A	brain
16	chr8:61655400-61660200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr8:61655600-61660200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr8:61655600-61663400	Weak transcription	Dnd41	blood
19	chr8:61655600-61663800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr8:61655600-61663800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr8:61655600-61664000	Weak transcription	HSMMtube	muscle
22	chr8:61655600-61664200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr8:61655600-61664200	Weak transcription	Spleen	Spleen
24	chr8:61655600-61671400	Weak transcription	Hela-S3	cervix
25	chr8:61655800-61660200	Weak transcription	Fetal Thymus	thymus
26	chr8:61655800-61660600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr8:61655800-61664000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr8:61655800-61664000	Weak transcription	Fetal Kidney	kidney
29	chr8:61655800-61664400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr8:61655800-61666200	Weak transcription	Lung	lung
31	chr8:61656000-61658400	Weak transcription	Esophagus	oesophagus
32	chr8:61656000-61660000	Weak transcription	Primary T cells from cord blood	blood
33	chr8:61656000-61663400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr8:61656000-61663600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr8:61656000-61663800	Weak transcription	GM12878-XiMat	blood
36	chr8:61656000-61664000	Weak transcription	Fetal Stomach	stomach
37	chr8:61656000-61664600	Weak transcription	Fetal Brain Male	brain
38	chr8:61656000-61678000	Weak transcription	Fetal Intestine Small	intestine
39	chr8:61656200-61660200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr8:61656200-61661000	Weak transcription	Brain Angular Gyrus	brain
41	chr8:61656200-61664200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr8:61656800-61663200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr8:61656800-61663800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr8:61656800-61664200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr8:61656800-61664800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr8:61657000-61660200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr8:61657000-61660200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr8:61657000-61660200	Weak transcription	Brain Germinal Matrix	brain
49	chr8:61657000-61660200	Weak transcription	Fetal Heart	heart
50	chr8:61657000-61660200	Weak transcription	Psoas Muscle	Psoas

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