Variant report

Variant	rs595874
Chromosome Location	chr17:46233445-46233446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46224894..46227721-chr17:46229708..46233601,3	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1039840	0.90[YRI][hapmap]
rs10853093	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs11079815	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11079817	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11655781	0.90[YRI][hapmap]
rs12452103	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1349676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1377201	1.00[CHB][hapmap]
rs1452661	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16954700	0.89[YRI][hapmap]
rs16954904	0.90[YRI][hapmap]
rs16954931	0.90[YRI][hapmap]
rs16955493	0.90[YRI][hapmap]
rs188268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1910574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208006	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs208007	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]
rs208013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2123342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2325886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28439030	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28551638	0.90[EUR][1000 genomes]
rs2924253	1.00[CHB][hapmap];0.90[YRI][hapmap]
rs2924255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2924256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2924258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2938471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs2938480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2938482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957932	1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs2957933	1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs3792693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4794426	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4794427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4794467	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794488	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4794561	0.90[YRI][hapmap]
rs5016303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7207270	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213530	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7216766	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7217741	0.85[YRI][hapmap]
rs7218167	0.90[YRI][hapmap]
rs7220940	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7225140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8066529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8067485	0.90[YRI][hapmap]
rs8071262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8077814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8081199	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8182234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9303543	0.95[YRI][hapmap]
rs9303544	0.90[YRI][hapmap]
rs979746	1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs9893405	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9899753	1.00[JPT][hapmap];0.94[YRI][hapmap]
rs9904487	0.90[YRI][hapmap]
rs9911479	0.90[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 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	chr17:46200400-46236600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr17:46212400-46234800	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr17:46216600-46235600	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr17:46220800-46249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:46221600-46238400	Weak transcription	Fetal Thymus	thymus
7	chr17:46222800-46234600	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr17:46226400-46234600	Strong transcription	Primary T cells from cord blood	blood
9	chr17:46227000-46233600	Weak transcription	Spleen	Spleen
10	chr17:46228400-46236600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr17:46230200-46237400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:46230600-46245000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr17:46230800-46234200	Strong transcription	Thymus	Thymus
14	chr17:46231000-46236600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr17:46231000-46243800	Weak transcription	Primary B cells from cord blood	blood
16	chr17:46231400-46234200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
17	chr17:46231600-46234400	Strong transcription	GM12878-XiMat	blood
18	chr17:46231800-46233600	Weak transcription	Fetal Kidney	kidney
19	chr17:46231800-46233800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr17:46231800-46233800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:46231800-46235200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:46231800-46238200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr17:46232000-46233800	Weak transcription	K562	blood
24	chr17:46232000-46236600	Weak transcription	A549	lung
25	chr17:46232000-46238000	Weak transcription	Pancreas	Pancrea
26	chr17:46232000-46239000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr17:46232000-46239800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr17:46232400-46237000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr17:46232600-46235400	Weak transcription	Fetal Intestine Large	intestine
30	chr17:46232800-46234600	Genic enhancers	Liver	Liver
31	chr17:46233000-46234000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr17:46233000-46234600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr17:46233200-46233600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
34	chr17:46233200-46233800	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr17:46233200-46234000	Enhancers	Primary hematopoietic stem cells	blood
36	chr17:46233200-46234000	Enhancers	HSMMtube	muscle
37	chr17:46233200-46234200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr17:46233200-46234200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:46233200-46234200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr17:46233200-46234200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:46233200-46234200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr17:46233200-46234200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
43	chr17:46233200-46234200	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr17:46233200-46234400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr17:46233400-46233800	Bivalent Enhancer	Fetal Brain Female	brain
46	chr17:46233400-46234200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr17:46233400-46234200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr17:46233400-46234200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr17:46233400-46234400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
50	chr17:46233400-46234400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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