Variant report

Variant	rs1829543
Chromosome Location	chr15:56496582-56496583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56492206..56494642-chr15:56495488..56498069,2	MCF-7	breast:
2	chr15:56494171..56496972-chr15:56541763..56543619,2	K562	blood:
3	chr15:56495337..56498069-chr15:56534935..56537509,2	K562	blood:

Variant related genes	Relation type
ENSG00000181827	Chromatin interaction
ENSG00000151575	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10152826	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10162834	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10163161	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10438327	0.88[CEU][hapmap];0.80[TSI][hapmap]
rs1072358	0.81[EUR][1000 genomes]
rs11632218	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11853962	0.92[CEU][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs11858173	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11858245	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12898789	0.81[EUR][1000 genomes]
rs12899534	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12907445	0.81[EUR][1000 genomes]
rs12909153	0.80[EUR][1000 genomes]
rs13379820	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1426070	0.81[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs17238601	1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs17238691	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs17819444	0.80[EUR][1000 genomes]
rs2247838	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2414466	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs2460649	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465405	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2465969	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554287	0.92[CEU][hapmap];0.80[TSI][hapmap]
rs2584689	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682030	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682032	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2682048	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2682055	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2713922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2713934	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2713937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2713939	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2718921	0.92[CEU][hapmap]
rs2718924	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2718947	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2725856	0.92[CEU][hapmap]
rs2947023	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34544252	0.80[EUR][1000 genomes]
rs35131119	0.81[EUR][1000 genomes]
rs35187662	0.81[EUR][1000 genomes]
rs35840822	0.84[EUR][1000 genomes]
rs36082281	0.80[EUR][1000 genomes]
rs4774852	0.86[AMR][1000 genomes]
rs4774854	0.92[CEU][hapmap]
rs56274791	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61010710	0.86[AMR][1000 genomes]
rs62044114	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6493836	0.89[ASN][1000 genomes]
rs6493844	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7163807	0.92[CEU][hapmap]
rs748344	0.92[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs767142	0.81[EUR][1000 genomes]
rs8032826	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8041422	0.88[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs894415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519725	chr15:56485598-56496582	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv528965	chr15:56489159-56504598	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56453600-56515000	Weak transcription	NHLF	lung
2	chr15:56457400-56500400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:56459200-56511000	Weak transcription	Esophagus	oesophagus
4	chr15:56463600-56496600	Weak transcription	NHEK	skin
5	chr15:56464600-56497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:56465400-56496600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:56465800-56496600	Weak transcription	HMEC	breast
8	chr15:56466000-56497000	Weak transcription	HSMMtube	muscle
9	chr15:56466000-56500000	Weak transcription	Thymus	Thymus
10	chr15:56466000-56514200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:56467000-56500400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:56467000-56511600	Weak transcription	Fetal Intestine Small	intestine
13	chr15:56470200-56498800	Weak transcription	Dnd41	blood
14	chr15:56470800-56503800	Weak transcription	Fetal Lung	lung
15	chr15:56477000-56500400	Weak transcription	Liver	Liver
16	chr15:56477200-56497000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:56480000-56496600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr15:56480000-56500000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr15:56480200-56497000	Weak transcription	HUVEC	blood vessel
20	chr15:56480200-56515400	Weak transcription	Hela-S3	cervix
21	chr15:56481400-56497800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:56482600-56497000	Weak transcription	NH-A	brain
23	chr15:56482600-56500200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:56484800-56500000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:56485000-56502800	Weak transcription	Gastric	stomach
26	chr15:56485600-56500000	Weak transcription	Aorta	Aorta
27	chr15:56485600-56521200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:56486600-56497000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:56486800-56496600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:56488200-56497000	Weak transcription	HSMM	muscle
31	chr15:56488400-56496800	Weak transcription	Fetal Brain Male	brain
32	chr15:56489200-56497200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:56489200-56503600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr15:56490600-56497400	Weak transcription	HepG2	liver
35	chr15:56490800-56497000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:56491600-56497000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr15:56491600-56497400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:56492000-56496800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr15:56492200-56497200	Weak transcription	A549	lung
40	chr15:56492400-56497400	Weak transcription	Primary T cells from cord blood	blood
41	chr15:56493000-56500000	Weak transcription	Ovary	ovary
42	chr15:56493200-56515400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:56493600-56497600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr15:56494800-56497200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:56494800-56497400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr15:56495000-56496800	Enhancers	K562	blood
47	chr15:56495000-56500000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:56495200-56496600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:56495200-56496600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:56495200-56497200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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