Variant report

Variant	rs16945753
Chromosome Location	chr17:60062592-60062593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60060416..60064562-chr17:60068573..60072345,4	MCF-7	breast:
2	chr17:60057894..60059644-chr17:60062477..60064261,2	K562	blood:
3	chr17:60056360..60059344-chr17:60060297..60063988,4	MCF-7	breast:
4	chr17:60061411..60063882-chr17:60065519..60067724,2	MCF-7	breast:
5	chr17:60048420..60050765-chr17:60062376..60064938,2	MCF-7	breast:
6	chr17:60061886..60064486-chr17:60102095..60103985,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10512492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079459	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12450223	0.86[ASN][1000 genomes]
rs12450560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12451910	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs12452094	1.00[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12452742	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs12600620	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12600909	0.91[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs12604037	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16945692	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs16945756	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16945759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16945801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271576	0.90[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2278812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs28654524	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3744434	0.90[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes]
rs3809753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3826419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4410139	0.86[EUR][1000 genomes]
rs4422036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4968408	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4968451	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs4968455	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs4968456	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs4968457	0.91[CEU][hapmap];0.82[JPT][hapmap]
rs4968460	0.90[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4968461	1.00[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4968462	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]
rs4968463	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968464	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4968467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968470	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968476	0.91[CEU][hapmap]
rs4988344	0.91[CEU][hapmap];0.87[YRI][hapmap]
rs56794817	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57137451	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57746689	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58241345	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58335059	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59080342	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60053512	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61469058	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61658218	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6504084	0.90[CEU][hapmap]
rs7218724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7221089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843781	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs73334621	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73336436	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8065778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8080599	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs8081917	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs9630736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60018000-60072800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr17:60018000-60073400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:60018600-60072600	Strong transcription	Fetal Thymus	thymus
4	chr17:60018800-60073600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:60020400-60073200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:60020600-60073000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr17:60020800-60073800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr17:60021200-60097000	Strong transcription	Dnd41	blood
9	chr17:60021800-60073600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr17:60025400-60074200	Strong transcription	Liver	Liver
11	chr17:60025400-60107600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
13	chr17:60034800-60072800	Strong transcription	Placenta	Placenta
14	chr17:60035800-60064400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr17:60036000-60074000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:60036400-60070000	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr17:60042600-60063600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr17:60042800-60105200	Weak transcription	Psoas Muscle	Psoas
19	chr17:60046400-60062800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr17:60048400-60072800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr17:60048600-60074200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr17:60048800-60097600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr17:60050200-60100800	Weak transcription	Small Intestine	intestine
24	chr17:60051600-60073800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr17:60051800-60073600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr17:60052000-60070400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr17:60052600-60072800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr17:60052600-60073400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr17:60052800-60063000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:60053400-60070600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr17:60053600-60063400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr17:60053600-60063600	Strong transcription	HMEC	breast
33	chr17:60053600-60065000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr17:60053600-60066400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr17:60053600-60073600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr17:60053800-60066600	Strong transcription	GM12878-XiMat	blood
37	chr17:60053800-60073200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr17:60054000-60062600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr17:60054000-60065400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr17:60054000-60074000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr17:60054200-60072200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr17:60055200-60063800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr17:60055200-60064000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr17:60055200-60066200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr17:60055200-60074000	Strong transcription	Primary T cells from cord blood	blood
46	chr17:60055400-60070200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr17:60055400-60072600	Strong transcription	Fetal Intestine Large	intestine
48	chr17:60055600-60072800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr17:60055600-60073800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr17:60055800-60064400	Strong transcription	A549	lung

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