Variant report

Variant	rs4968462
Chromosome Location	chr17:60019012-60019013
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60003740..60007255-chr17:60016525..60022639,9	MCF-7	breast:
2	chr17:60001930..60007756-chr17:60014153..60029774,25	MCF-7	breast:
3	chr17:60018036..60020087-chr17:60133824..60135422,2	MCF-7	breast:
4	chr17:60008585..60011122-chr17:60017280..60019717,2	MCF-7	breast:
5	chr17:60017040..60020796-chr17:60041060..60043758,3	K562	blood:
6	chr17:60017329..60019880-chr17:60023720..60025773,3	K562	blood:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10512492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11079459	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12450560	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12451910	0.82[JPT][hapmap]
rs12452094	0.82[CEU][hapmap];0.83[JPT][hapmap];0.84[AFR][1000 genomes]
rs12452732	0.84[AFR][1000 genomes]
rs12452742	0.82[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12600620	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12600909	0.82[JPT][hapmap]
rs12604037	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs16945692	0.81[JPT][hapmap]
rs16945753	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs16945756	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16945759	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16945801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2271576	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2278812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28654524	0.84[AFR][1000 genomes]
rs3744434	0.82[JPT][hapmap]
rs3809753	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3826419	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4422036	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4968408	0.82[JPT][hapmap];0.88[AFR][1000 genomes]
rs4968451	0.87[YRI][hapmap]
rs4968455	0.83[JPT][hapmap]
rs4968456	0.83[JPT][hapmap]
rs4968457	0.81[JPT][hapmap]
rs4968460	0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4968461	0.82[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4968463	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968464	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4968467	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4968468	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4988344	0.87[YRI][hapmap]
rs56794817	0.82[AFR][1000 genomes]
rs57137451	0.84[AFR][1000 genomes]
rs57746689	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs58241345	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs58335059	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59080342	1.00[AFR][1000 genomes]
rs60053512	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61658218	0.81[AMR][1000 genomes]
rs7218724	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7221089	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs73334621	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs8065778	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8066964	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8074890	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs8080599	0.81[JPT][hapmap]
rs8081917	0.82[JPT][hapmap]
rs9630736	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]

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:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60005800-60022000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr17:60005800-60022000	Weak transcription	Thymus	Thymus
3	chr17:60005800-60022800	Weak transcription	Brain Angular Gyrus	brain
4	chr17:60006000-60019400	Weak transcription	Hela-S3	cervix
5	chr17:60006000-60019600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr17:60006000-60020400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr17:60006000-60020800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr17:60006000-60021000	Weak transcription	HMEC	breast
9	chr17:60006000-60021200	Weak transcription	Osteobl	bone
10	chr17:60006000-60021400	Weak transcription	HUVEC	blood vessel
11	chr17:60006000-60022000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr17:60006000-60022000	Weak transcription	Fetal Brain Female	brain
13	chr17:60006000-60022000	Weak transcription	HSMMtube	muscle
14	chr17:60006000-60022800	Weak transcription	Brain Anterior Caudate	brain
15	chr17:60006000-60023000	Weak transcription	Brain Hippocampus Middle	brain
16	chr17:60006000-60023600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr17:60012800-60023800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:60013200-60021000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr17:60013400-60021400	Weak transcription	NHDF-Ad	bronchial
20	chr17:60013800-60021600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr17:60014200-60021200	Weak transcription	Dnd41	blood
22	chr17:60014200-60030000	Weak transcription	Stomach Mucosa	stomach
23	chr17:60014400-60020400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr17:60014400-60022000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr17:60014400-60022200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr17:60014600-60024400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr17:60014800-60019200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr17:60014800-60020200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr17:60014800-60020600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:60014800-60023800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr17:60014800-60028000	Weak transcription	Colonic Mucosa	Colon
32	chr17:60015000-60022800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr17:60015400-60021200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr17:60015400-60022200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr17:60015400-60023400	Weak transcription	NHLF	lung
36	chr17:60015400-60023800	Weak transcription	Fetal Intestine Small	intestine
37	chr17:60015600-60021800	Weak transcription	HepG2	liver
38	chr17:60015600-60022400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr17:60015800-60019600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr17:60015800-60021800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr17:60016000-60023600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr17:60016000-60029800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr17:60016200-60019600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr17:60016200-60023800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr17:60016200-60024200	Weak transcription	Lung	lung
46	chr17:60016400-60021400	Weak transcription	GM12878-XiMat	blood
47	chr17:60016400-60027800	Weak transcription	Right Ventricle	heart
48	chr17:60016600-60021000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr17:60016600-60022000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr17:60016600-60022000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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