Variant report

Variant	rs12601012
Chromosome Location	chr17:67149557-67149558
allele	A/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	chr17:67149484-67149566	MCF-7	breast:	n/a	n/a
2	POLR2A	chr17:67149464-67149616	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:67148089..67149780-chr17:67219261..67221690,2	MCF-7	breast:
2	chr17:67084611..67087550-chr17:67148578..67150089,2	K562	blood:

Variant related genes	Relation type
ABCA10	TF binding region
ENSG00000154263	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10491178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656320	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12103556	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12600759	0.83[ASN][1000 genomes]
rs12602007	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12602396	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs12602766	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12602816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12602962	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12604047	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938420	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12945932	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12948410	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1468514	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16973562	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs16973656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973672	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16973722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16973774	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1860120	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1968099	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2233767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2233768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286419	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2302289	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2886048	0.90[CHB][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35991088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36145749	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3891333	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41496448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968787	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968837	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4968844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968853	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968996	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55821831	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57736258	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58452744	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58761646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6502001	1.00[CHB][hapmap]
rs6502002	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6502005	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7209351	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7212506	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7212963	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73356149	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs736528	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7501583	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7501929	1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs764178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8065842	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8067965	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8068468	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8080508	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8081118	1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8082114	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9282553	0.90[CHB][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9282554	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9282555	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9889289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9896308	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9904389	0.89[EUR][1000 genomes]
rs9905622	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9909265	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	nsv575930	chr17:67120025-67212031	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67114600-67162800	Weak transcription	Brain Angular Gyrus	brain
2	chr17:67124800-67150000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:67127000-67150600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr17:67132000-67151600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr17:67138000-67154000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr17:67138200-67150600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr17:67138200-67151200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr17:67138200-67151600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:67138200-67152200	Weak transcription	Fetal Muscle Leg	muscle
10	chr17:67138600-67155400	Weak transcription	Brain Anterior Caudate	brain
11	chr17:67138800-67152000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr17:67138800-67162800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr17:67138800-67182000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr17:67140200-67154000	Weak transcription	Fetal Lung	lung
15	chr17:67141600-67155400	Weak transcription	Colon Smooth Muscle	Colon
16	chr17:67141800-67171800	Weak transcription	GM12878-XiMat	blood
17	chr17:67142200-67152400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr17:67142400-67151000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr17:67143800-67154200	Weak transcription	Right Ventricle	heart
20	chr17:67144000-67151600	Weak transcription	Fetal Intestine Large	intestine
21	chr17:67144000-67163200	Weak transcription	Left Ventricle	heart
22	chr17:67144000-67175800	Weak transcription	Gastric	stomach
23	chr17:67144000-67236000	Weak transcription	Psoas Muscle	Psoas
24	chr17:67144800-67150400	Strong transcription	Liver	Liver
25	chr17:67145000-67150200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr17:67147400-67150800	Strong transcription	Ovary	ovary
27	chr17:67147600-67150800	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr17:67147600-67151400	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr17:67147800-67150600	Strong transcription	Adipose Nuclei	Adipose
30	chr17:67148200-67150800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr17:67148400-67171600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:67148600-67150200	Strong transcription	Fetal Intestine Small	intestine
33	chr17:67148600-67175600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr17:67148800-67190200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr17:67149400-67149600	Strong transcription	Pancreas	Pancrea

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