Variant report

Variant	rs4968408
Chromosome Location	chr17:59963911-59963912
allele	C/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	chr17:59963321-59965798	K562	blood:	n/a	n/a
2	POLR2A	chr17:59963868-59963941	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:59963085..59966106-chr20:54151833..54153600,3	MCF-7	breast:

Variant related genes	Relation type
INTS2	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10512492	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs11079459	0.88[AFR][1000 genomes]
rs12450560	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12451910	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12452094	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12452732	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12452742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12600909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12604037	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs16945692	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16945753	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs16945759	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs16945801	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs2271576	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278812	0.88[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap]
rs2378908	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs3744434	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3809753	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs3826419	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4422036	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs4968451	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968452	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4968454	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968456	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968459	0.83[ASN][1000 genomes]
rs4968460	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968461	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4968462	0.82[JPT][hapmap];0.88[AFR][1000 genomes]
rs4968463	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4968464	0.84[AFR][1000 genomes]
rs4968467	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4968468	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs4988344	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56794817	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58085921	0.84[ASN][1000 genomes]
rs58624595	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59080342	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61169879	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61658218	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7218724	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7221089	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs73332565	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73332580	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73332598	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73334621	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8065778	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs8066964	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs8074890	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs8080599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8081917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9630735	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9630736	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59941200-59964600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:59941400-59965400	Weak transcription	Lung	lung
3	chr17:59941400-59975000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:59941400-60004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:59941400-60004400	Weak transcription	Aorta	Aorta
6	chr17:59941400-60004400	Weak transcription	Pancreas	Pancrea
7	chr17:59941600-59965200	Weak transcription	Psoas Muscle	Psoas
8	chr17:59941600-59965400	Weak transcription	Brain Substantia Nigra	brain
9	chr17:59941600-59965600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr17:59941600-59966800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:59941600-59979600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr17:59941600-59987600	Weak transcription	Right Ventricle	heart
13	chr17:59941600-60003600	Weak transcription	Stomach Mucosa	stomach
14	chr17:59941600-60004400	Weak transcription	Colonic Mucosa	Colon
15	chr17:59941800-59967000	Weak transcription	Fetal Brain Male	brain
16	chr17:59941800-59968800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr17:59941800-59969200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr17:59941800-59971800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr17:59941800-59979200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr17:59941800-59979200	Weak transcription	Brain Angular Gyrus	brain
21	chr17:59942600-60002800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:59943600-59989600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:59944400-59970000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr17:59944600-59967600	Strong transcription	HepG2	liver
25	chr17:59946600-59989200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:59947400-59977400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr17:59948000-59964000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr17:59948000-59965400	Weak transcription	Ovary	ovary
29	chr17:59948000-59972600	Weak transcription	NHDF-Ad	bronchial
30	chr17:59948000-59981800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr17:59948200-59980600	Weak transcription	HMEC	breast
32	chr17:59948200-59986800	Weak transcription	Fetal Kidney	kidney
33	chr17:59949400-59966800	Weak transcription	NH-A	brain
34	chr17:59949800-59965600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr17:59949800-59966800	Weak transcription	K562	blood
36	chr17:59949800-59967000	Weak transcription	Colon Smooth Muscle	Colon
37	chr17:59950000-59979200	Weak transcription	NHLF	lung
38	chr17:59950800-59968800	Strong transcription	Adipose Nuclei	Adipose
39	chr17:59950800-59981600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr17:59951000-59972400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr17:59951400-59992200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr17:59951600-59989600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr17:59952000-59969200	Weak transcription	HUVEC	blood vessel
44	chr17:59952000-59971600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr17:59952600-59964800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr17:59952800-59981400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr17:59953200-59968200	Strong transcription	Fetal Muscle Leg	muscle
48	chr17:59953200-59972200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr17:59953800-59985600	Weak transcription	Small Intestine	intestine
50	chr17:59954400-60003800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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