Variant report

Variant	rs7816621
Chromosome Location	chr8:61621506-61621507
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:61563492..61565513-chr8:61620455..61623990,3	MCF-7	breast:
2	chr8:61612592..61618600-chr8:61619190..61622495,7	MCF-7	breast:
3	chr8:61590260..61597729-chr8:61611560..61624694,18	MCF-7	breast:
4	chr8:61612691..61616083-chr8:61619050..61621954,3	K562	blood:
5	chr8:61619832..61624344-chr8:61624507..61628732,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171316	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10093135	0.84[ASN][1000 genomes]
rs1038352	0.81[ASN][1000 genomes]
rs10808711	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10808712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10808713	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs10957154	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10957155	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10957156	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10957158	0.81[ASN][1000 genomes]
rs11985638	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11990117	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11990495	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11991467	0.81[ASN][1000 genomes]
rs11992809	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs11993480	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11995234	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11997122	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12544305	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12681737	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13255519	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs13264014	0.84[ASN][1000 genomes]
rs13277976	0.81[ASN][1000 genomes]
rs1384688	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1483206	0.84[ASN][1000 genomes]
rs16926407	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1905305	0.84[ASN][1000 genomes]
rs2035456	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2035457	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2054666	0.81[ASN][1000 genomes]
rs2054667	0.81[ASN][1000 genomes]
rs2128713	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2326598	0.81[ASN][1000 genomes]
rs2875984	0.81[ASN][1000 genomes]
rs4307377	0.89[CHB][hapmap]
rs4449834	0.89[CHB][hapmap]
rs4472560	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4500113	0.81[ASN][1000 genomes]
rs4526395	1.00[CHB][hapmap]
rs4737563	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4737565	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs4738815	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4738818	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4738821	0.81[ASN][1000 genomes]
rs4738822	0.81[ASN][1000 genomes]
rs4738824	0.81[ASN][1000 genomes]
rs4738831	0.89[CHB][hapmap]
rs4738832	0.89[CHB][hapmap]
rs6471894	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6471896	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6471897	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6471898	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]
rs6471901	0.81[ASN][1000 genomes]
rs6471903	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs6471905	0.89[CHB][hapmap]
rs6988582	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs6994180	0.84[ASN][1000 genomes]
rs6995557	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7000766	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs7002806	0.81[ASN][1000 genomes]
rs7005873	0.89[CHB][hapmap]
rs7009754	0.81[ASN][1000 genomes]
rs7011972	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7012450	0.84[ASN][1000 genomes]
rs7017676	0.81[ASN][1000 genomes]
rs730085	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.81[ASN][1000 genomes]
rs7814114	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7816126	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7823484	0.81[ASN][1000 genomes]
rs7826035	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7834977	0.86[CHB][hapmap]
rs7836586	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs7838426	0.84[ASN][1000 genomes]
rs7840098	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7842389	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7842498	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7843033	0.81[ASN][1000 genomes]
rs7845701	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7846065	0.84[ASN][1000 genomes]
rs900502	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9298040	0.84[ASN][1000 genomes]
rs9643371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650201	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv824657	chr8:61555227-61626758	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	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
6	nsv1019809	chr8:61597918-61624034	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv539631	chr8:61597918-61624034	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv6219	chr8:61599770-61644558	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7816621	TOX	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61603400-61626200	Weak transcription	Fetal Thymus	thymus
2	chr8:61607400-61627000	Weak transcription	Spleen	Spleen
3	chr8:61612600-61622000	Enhancers	Primary B cells from peripheral blood	blood
4	chr8:61615600-61644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr8:61616200-61626000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr8:61617000-61621800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr8:61619000-61623200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr8:61619400-61623000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr8:61619600-61621600	Enhancers	Adipose Nuclei	Adipose
10	chr8:61619600-61621600	Enhancers	Liver	Liver
11	chr8:61619600-61621800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr8:61619800-61621600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr8:61619800-61621600	Weak transcription	Primary B cells from cord blood	blood
14	chr8:61619800-61621600	Enhancers	Brain Cingulate Gyrus	brain
15	chr8:61619800-61621600	Enhancers	Psoas Muscle	Psoas
16	chr8:61619800-61621800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:61619800-61621800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr8:61619800-61621800	Enhancers	HSMMtube	muscle
19	chr8:61619800-61622000	Enhancers	Brain Hippocampus Middle	brain
20	chr8:61619800-61622000	Enhancers	Fetal Lung	lung
21	chr8:61619800-61622000	Enhancers	Placenta Amnion	Placenta Amnion
22	chr8:61619800-61622200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr8:61619800-61622200	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr8:61620000-61621800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr8:61620000-61622000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr8:61620000-61624800	Weak transcription	GM12878-XiMat	blood
27	chr8:61620400-61621600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr8:61620400-61621600	Enhancers	H9 Cell Line	embryonic stem cell
29	chr8:61620400-61621600	Enhancers	Brain Angular Gyrus	brain
30	chr8:61620400-61621600	Enhancers	Duodenum Mucosa	Duodenum
31	chr8:61620400-61621600	Enhancers	Fetal Intestine Small	intestine
32	chr8:61620400-61621600	Enhancers	Fetal Muscle Leg	muscle
33	chr8:61620400-61621600	Enhancers	Gastric	stomach
34	chr8:61620400-61621600	Enhancers	Left Ventricle	heart
35	chr8:61620400-61621600	Enhancers	Right Ventricle	heart
36	chr8:61620400-61621600	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr8:61620400-61621600	Flanking Active TSS	Hela-S3	cervix
38	chr8:61620400-61621600	Flanking Active TSS	HMEC	breast
39	chr8:61620400-61621600	Enhancers	K562	blood
40	chr8:61620400-61621800	Enhancers	Brain Germinal Matrix	brain
41	chr8:61620400-61621800	Enhancers	Brain Substantia Nigra	brain
42	chr8:61620400-61622000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr8:61620400-61622000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr8:61620400-61622000	Enhancers	Brain Anterior Caudate	brain
45	chr8:61620400-61622000	Enhancers	Rectal Smooth Muscle	rectum
46	chr8:61620400-61622000	Enhancers	NHEK	skin
47	chr8:61620400-61622000	Enhancers	Osteobl	bone
48	chr8:61620400-61623400	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr8:61620600-61621600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr8:61620600-61621600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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