Variant report

Variant	rs9916693
Chromosome Location	chr17:67138563-67138564
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	chr17:67137535-67138914	MCF10A-Er-Src	breast:	n/a	n/a
2	TCF12	chr17:67138468-67139001	SK-N-SH	brain:	n/a	n/a
3	HNF4A	chr17:67138523-67138879	HepG2	liver:	n/a	chr17:67138750-67138765 chr17:67138750-67138765 chr17:67138749-67138764 chr17:67138751-67138763 chr17:67138750-67138765
4	TCF12	chr17:67138472-67139129	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr17:67137623-67138921	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr17:67137691-67138959	HUVEC	blood vessel:	n/a	n/a
7	STAT3	chr17:67137801-67138896	MCF10A-Er-Src	breast:	n/a	chr17:67138265-67138273
8	POLR2A	chr17:67138488-67138898	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:67138378..67141973-chr17:67143185..67146328,3	K562	blood:
2	chr17:67115279..67117551-chr17:67138552..67141546,2	K562	blood:

Variant related genes	Relation type
ABCA6	TF binding region
ENSG00000154263	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10775358	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs10775359	0.84[ASN][1000 genomes]
rs1158495	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs11652530	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11656539	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12162136	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12453914	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12601388	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12939282	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12940298	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12952117	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12953127	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1558166	0.87[ASN][1000 genomes]
rs16973567	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1968100	0.86[ASN][1000 genomes]
rs1974576	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1974577	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1990335	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2041170	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2041171	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108738	0.84[ASN][1000 genomes]
rs2190900	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2215148	0.86[ASN][1000 genomes]
rs2364986	0.87[ASN][1000 genomes]
rs2364993	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs3744489	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4141177	0.87[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4334355	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4577157	0.84[ASN][1000 genomes]
rs4603621	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968785	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4968838	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968839	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968843	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4968849	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs4968851	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs5025273	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs6501183	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7207609	0.91[EUR][1000 genomes]
rs7208586	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7210259	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs7213831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7214079	0.90[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7216899	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7217887	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs740518	0.87[ASN][1000 genomes]
rs740520	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7503217	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8064595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8066449	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs8074654	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs8077252	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8077551	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs8078314	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8079981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8080863	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs8081003	0.81[ASN][1000 genomes]
rs9303012	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs976698	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs981452	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9892172	0.86[ASN][1000 genomes]
rs9898868	0.86[ASN][1000 genomes]
rs9899837	0.86[ASN][1000 genomes]
rs9902643	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs9904672	0.86[ASN][1000 genomes]
rs9911770	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9912127	0.81[CHB][hapmap]
rs9916084	0.84[ASN][1000 genomes]
rs997781	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67096200-67143400	Weak transcription	Psoas Muscle	Psoas
2	chr17:67101200-67143400	Weak transcription	Pancreas	Pancrea
3	chr17:67114600-67162800	Weak transcription	Brain Angular Gyrus	brain
4	chr17:67124800-67150000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:67127000-67143400	Weak transcription	Fetal Intestine Large	intestine
6	chr17:67127000-67150600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:67130600-67146200	Weak transcription	Lung	lung
8	chr17:67132000-67151600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr17:67133800-67145600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr17:67134400-67143400	Weak transcription	Left Ventricle	heart
11	chr17:67134600-67145000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr17:67136200-67138800	Active TSS	Ovary	ovary
13	chr17:67136200-67138800	Active TSS	Right Atrium	heart
14	chr17:67136200-67139000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:67136400-67138800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:67136600-67138600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr17:67136600-67138800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:67136600-67138800	Active TSS	Fetal Lung	lung
19	chr17:67136800-67138800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr17:67136800-67138800	Active TSS	Stomach Smooth Muscle	stomach
21	chr17:67137200-67138600	Active TSS	Brain Substantia Nigra	brain
22	chr17:67137400-67138600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr17:67137400-67138600	Flanking Active TSS	Osteobl	bone
24	chr17:67137600-67138600	Active TSS	Brain Anterior Caudate	brain
25	chr17:67137600-67138600	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr17:67137600-67138600	Flanking Active TSS	HUVEC	blood vessel
27	chr17:67137600-67139000	Enhancers	HepG2	liver
28	chr17:67137600-67139200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr17:67137800-67138800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:67137800-67138800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr17:67137800-67138800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr17:67137800-67138800	Enhancers	HMEC	breast
33	chr17:67137800-67141200	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr17:67137800-67141400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr17:67138000-67138600	Enhancers	Stomach Mucosa	stomach
36	chr17:67138000-67138600	Enhancers	Hela-S3	cervix
37	chr17:67138000-67138800	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr17:67138000-67138800	Flanking Active TSS	Liver	Liver
39	chr17:67138000-67138800	Enhancers	Small Intestine	intestine
40	chr17:67138000-67138800	Flanking Active TSS	NHDF-Ad	bronchial
41	chr17:67138000-67139600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr17:67138000-67154000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr17:67138200-67138800	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr17:67138200-67139200	Weak transcription	Fetal Stomach	stomach
45	chr17:67138200-67143400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr17:67138200-67150600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr17:67138200-67151200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr17:67138200-67151600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr17:67138200-67152200	Weak transcription	Fetal Muscle Leg	muscle
50	chr17:67138400-67138800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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