Variant report

Variant	rs190039
Chromosome Location	chr15:57233498-57233499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57179564..57182313-chr15:57232225..57234178,2	K562	blood:
2	chr15:57210017..57214406-chr15:57230340..57233852,4	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1015967	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10438332	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11071302	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11071307	1.00[CEU][hapmap]
rs1139006	0.91[EUR][1000 genomes]
rs11630965	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11632502	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11632526	0.91[EUR][1000 genomes]
rs11636655	1.00[CEU][hapmap]
rs11856338	0.83[EUR][1000 genomes]
rs12148850	0.86[EUR][1000 genomes]
rs12437976	0.82[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12440219	0.88[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591367	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12595644	0.89[EUR][1000 genomes]
rs12902058	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs12906025	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs1346880	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs1367491	0.87[EUR][1000 genomes]
rs1625176	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1628974	0.93[EUR][1000 genomes]
rs1631079	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1642925	0.90[EUR][1000 genomes]
rs1642927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1642928	0.93[EUR][1000 genomes]
rs1642929	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1642935	0.89[EUR][1000 genomes]
rs1642936	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1642937	0.89[EUR][1000 genomes]
rs1642940	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs1652732	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1652737	0.89[EUR][1000 genomes]
rs1652738	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1652739	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1652740	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1652741	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1657926	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs169893	0.86[EUR][1000 genomes]
rs17239222	1.00[CEU][hapmap]
rs17819940	1.00[CEU][hapmap]
rs1820996	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1963831	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2111890	0.80[EUR][1000 genomes]
rs2111892	0.84[EUR][1000 genomes]
rs2116067	0.81[AMR][1000 genomes]
rs2126402	1.00[CEU][hapmap]
rs213148	0.91[EUR][1000 genomes]
rs213152	0.89[EUR][1000 genomes]
rs213160	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs213163	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs213166	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs213168	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2169468	1.00[CEU][hapmap]
rs2252289	0.95[CEU][hapmap]
rs2435905	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs2439921	0.98[EUR][1000 genomes]
rs2439925	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2464427	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs2464428	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs2470080	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2470081	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2470083	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2470084	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs2543675	0.82[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2566840	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2566844	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2566846	0.91[EUR][1000 genomes]
rs2566856	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2585076	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2585116	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703588	0.95[CEU][hapmap]
rs2733187	0.95[CEU][hapmap]
rs2915176	0.87[EUR][1000 genomes]
rs2920268	0.80[EUR][1000 genomes]
rs2920270	1.00[CEU][hapmap]
rs2920272	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2951900	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2951902	0.95[CEU][hapmap]
rs2957573	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2957576	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2957578	0.95[CEU][hapmap]
rs2957592	1.00[CEU][hapmap]
rs2962994	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs2962995	1.00[CEU][hapmap]
rs34373044	0.81[AMR][1000 genomes]
rs4774246	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs4774900	0.81[AMR][1000 genomes]
rs55886927	0.84[EUR][1000 genomes]
rs7162730	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7164742	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs7168945	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs7183392	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs72749478	0.89[EUR][1000 genomes]
rs72749491	0.91[EUR][1000 genomes]
rs7359192	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs8029445	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs8031788	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8042190	1.00[CEU][hapmap]
rs9806712	1.00[CEU][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57212400-57256000	Weak transcription	Pancreas	Pancrea
2	chr15:57212600-57241000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:57213200-57256000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:57216400-57241800	Weak transcription	Fetal Brain Male	brain
5	chr15:57220400-57236400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:57222600-57250200	Weak transcription	NH-A	brain
7	chr15:57222800-57240800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:57222800-57255000	Weak transcription	HMEC	breast
9	chr15:57223000-57236800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:57223200-57240400	Weak transcription	Aorta	Aorta
11	chr15:57224400-57234400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:57224400-57235200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:57224400-57238000	Weak transcription	Fetal Lung	lung
14	chr15:57224600-57233800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:57224600-57248600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:57225000-57239400	Weak transcription	Left Ventricle	heart
17	chr15:57225000-57244200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:57225000-57249000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:57225200-57238000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr15:57226400-57234000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:57226400-57235200	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:57226400-57242000	Weak transcription	HUVEC	blood vessel
23	chr15:57226600-57234600	Weak transcription	Fetal Heart	heart
24	chr15:57227000-57249800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr15:57227200-57234200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr15:57227200-57236800	Weak transcription	A549	lung
27	chr15:57227600-57234000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:57227600-57234000	Weak transcription	Brain Germinal Matrix	brain
29	chr15:57227600-57235400	Weak transcription	Dnd41	blood
30	chr15:57227600-57236000	Weak transcription	Psoas Muscle	Psoas
31	chr15:57227600-57260600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:57227800-57235200	Weak transcription	NHEK	skin
33	chr15:57228000-57234600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:57228000-57235200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:57228000-57237600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr15:57228000-57237600	Weak transcription	Fetal Intestine Large	intestine
37	chr15:57228000-57238000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr15:57228000-57242400	Weak transcription	Fetal Intestine Small	intestine
39	chr15:57228200-57235400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:57228200-57236800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:57228200-57238000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:57228200-57260600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:57228400-57236800	Weak transcription	Primary B cells from cord blood	blood
44	chr15:57228400-57237600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:57228800-57234200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:57229200-57233800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr15:57229200-57235400	Weak transcription	Fetal Brain Female	brain
48	chr15:57229200-57237400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:57229200-57237600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:57229400-57255800	Weak transcription	Fetal Stomach	stomach

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