Variant report

Variant	rs6502001
Chromosome Location	chr17:67096079-67096080
allele	G/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	CTCF	chr17:67095980-67096130	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:67096035..67097886-chr17:67098176..67100772,2	K562	blood:
2	chr17:67087494..67092191-chr17:67094325..67097858,5	K562	blood:

Variant related genes	Relation type
ABCA6	TF binding region
ENSG00000267361	TF binding region
ENSG00000267361	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10491178	0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[TSI][hapmap]
rs11077946	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs11656320	0.94[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];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12103556	0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[TSI][hapmap]
rs12601012	1.00[CHB][hapmap]
rs12602396	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12602816	0.91[CHB][hapmap]
rs1468514	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs16973562	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs16973656	0.91[CHB][hapmap]
rs16973722	0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[TSI][hapmap]
rs16973774	0.81[CHB][hapmap]
rs1860120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2233767	0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[TSI][hapmap]
rs2233768	0.90[CHB][hapmap]
rs2286419	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2302289	1.00[CEU][hapmap]
rs2886048	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs35991088	0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[TSI][hapmap]
rs41496448	0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[TSI][hapmap]
rs4968786	0.91[CHB][hapmap]
rs4968844	0.91[CHB][hapmap]
rs4968996	1.00[CEU][hapmap]
rs6502002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6502005	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap]
rs7209351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7212506	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs736528	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs758255	0.85[CEU][hapmap];1.00[TSI][hapmap]
rs764178	0.91[CHB][hapmap]
rs8067965	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs8068468	0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[TSI][hapmap]
rs8080508	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs8081118	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap]
rs8082114	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap]
rs9282553	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9282554	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs9889289	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833526	chr17:66980758-67137034	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv908705	chr17:67061898-67112456	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	esv1850212	chr17:67081732-67117428	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv470598	chr17:67081830-67212595	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67067200-67099600	Weak transcription	Gastric	stomach
2	chr17:67067200-67111600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr17:67076800-67109800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr17:67077800-67137800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr17:67079400-67112200	Strong transcription	Liver	Liver
6	chr17:67079400-67112600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:67079400-67117600	Weak transcription	Esophagus	oesophagus
8	chr17:67079600-67101200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr17:67079600-67114200	Weak transcription	NHDF-Ad	bronchial
10	chr17:67080800-67112000	Weak transcription	Brain Substantia Nigra	brain
11	chr17:67081200-67102000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr17:67081400-67118600	Weak transcription	Right Ventricle	heart
13	chr17:67082200-67114400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr17:67085800-67099600	Weak transcription	Lung	lung
15	chr17:67087000-67114600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr17:67087000-67130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr17:67089600-67097200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr17:67089800-67102200	Weak transcription	GM12878-XiMat	blood
19	chr17:67090400-67110000	Strong transcription	Adipose Nuclei	Adipose
20	chr17:67091200-67131400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr17:67091600-67104400	Weak transcription	Left Ventricle	heart
22	chr17:67091600-67130000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr17:67092200-67137600	Weak transcription	Brain Anterior Caudate	brain
24	chr17:67095000-67096400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr17:67095000-67096600	Enhancers	K562	blood
26	chr17:67095000-67097400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr17:67095200-67098600	Strong transcription	Fetal Lung	lung
28	chr17:67095600-67096200	Enhancers	Psoas Muscle	Psoas
29	chr17:67095600-67096400	Strong transcription	Ovary	ovary
30	chr17:67095600-67096800	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr17:67095800-67096400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr17:67095800-67097200	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr17:67095800-67131000	Weak transcription	Fetal Muscle Leg	muscle

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