Variant report

Variant	rs2962988
Chromosome Location	chr15:57380937-57380938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57370971..57373246-chr15:57380194..57383118,2	K562	blood:
2	chr15:57364693..57367235-chr15:57380279..57382303,2	K562	blood:
3	chr15:57370291..57372471-chr15:57379533..57381694,2	K562	blood:

Extended variants
information (count: 102 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1015967	0.86[JPT][hapmap]
rs10438332	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs11071307	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs11071310	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs11632502	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs11632526	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs11636655	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12324235	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12591367	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs12593843	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12595074	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1346880	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs1625176	0.85[JPT][hapmap]
rs1631079	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs1642936	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs1642940	0.86[JPT][hapmap]
rs1652732	0.86[JPT][hapmap]
rs1652738	0.85[JPT][hapmap]
rs1652739	0.85[JPT][hapmap]
rs1652740	0.86[JPT][hapmap]
rs1652741	0.86[JPT][hapmap]
rs1657926	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs17239222	1.00[YRI][hapmap]
rs17239459	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs17819940	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs17820018	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs17820095	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs1820996	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs1867638	0.93[JPT][hapmap]
rs1870870	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2126402	1.00[YRI][hapmap]
rs213160	0.86[JPT][hapmap]
rs213163	0.84[JPT][hapmap]
rs213166	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs213168	0.86[JPT][hapmap]
rs2169468	1.00[YRI][hapmap]
rs2248620	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2252289	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2290939	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2431032	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2435905	0.85[JPT][hapmap]
rs2439917	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2464427	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2464428	0.92[JPT][hapmap];1.00[YRI][hapmap]
rs2470080	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2470081	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2470083	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2470084	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2470085	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2566844	0.85[JPT][hapmap]
rs2566856	1.00[YRI][hapmap]
rs2585076	0.85[JPT][hapmap]
rs2585116	0.85[JPT][hapmap]
rs2591062	0.93[JPT][hapmap]
rs2591066	0.93[JPT][hapmap]
rs2593217	0.81[JPT][hapmap]
rs2593221	0.93[JPT][hapmap]
rs2593234	0.93[JPT][hapmap]
rs2593236	0.93[JPT][hapmap]
rs2615228	0.93[JPT][hapmap]
rs2703588	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2703599	0.93[JPT][hapmap]
rs2703600	0.86[JPT][hapmap]
rs2733187	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2733309	0.93[JPT][hapmap]
rs2733318	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2733320	0.93[JPT][hapmap]
rs2733330	0.93[JPT][hapmap]
rs2920270	1.00[YRI][hapmap]
rs2920272	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2951900	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2951902	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2951905	0.81[AMR][1000 genomes]
rs2951907	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2957573	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2957576	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2957578	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2957592	1.00[YRI][hapmap]
rs2962994	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2962995	1.00[YRI][hapmap]
rs3794617	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs55910715	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6493909	0.86[JPT][hapmap]
rs7167268	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs7182038	0.93[JPT][hapmap]
rs7182188	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs7183392	0.86[JPT][hapmap]
rs72751006	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72751008	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72751021	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs734033	0.82[JPT][hapmap]
rs7359192	0.86[JPT][hapmap]
rs8023315	1.00[YRI][hapmap]
rs8024830	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs8029445	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs8037987	0.93[JPT][hapmap]
rs8042322	0.93[JPT][hapmap]
rs8043103	0.93[JPT][hapmap]
rs9806712	0.86[JPT][hapmap]

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	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
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
2	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:57354200-57384600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:57356000-57393400	Weak transcription	Thymus	Thymus
5	chr15:57362800-57384200	Weak transcription	HepG2	liver
6	chr15:57363800-57382000	Weak transcription	Right Atrium	heart
7	chr15:57365200-57384000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:57365600-57385200	Weak transcription	HSMM	muscle
9	chr15:57365800-57384000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:57371800-57382400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:57372000-57384000	Weak transcription	Dnd41	blood
12	chr15:57372600-57386000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:57372600-57404000	Weak transcription	HSMMtube	muscle
14	chr15:57372600-57404200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:57372800-57384000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:57372800-57384000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr15:57372800-57384400	Weak transcription	Liver	Liver
18	chr15:57372800-57386000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:57372800-57410200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:57373000-57382000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:57373000-57384600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr15:57373000-57385400	Weak transcription	Primary B cells from cord blood	blood
23	chr15:57373200-57381400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:57373200-57384200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr15:57373200-57384600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr15:57374000-57385000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr15:57374400-57382000	Weak transcription	Psoas Muscle	Psoas
28	chr15:57374400-57389400	Weak transcription	NHEK	skin
29	chr15:57374600-57382200	Weak transcription	Left Ventricle	heart
30	chr15:57374600-57382600	Weak transcription	Adipose Nuclei	Adipose
31	chr15:57374600-57384000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:57374600-57386000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:57374600-57390000	Weak transcription	HMEC	breast
34	chr15:57374600-57398600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr15:57374800-57384400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:57374800-57386800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:57374800-57387800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:57374800-57397800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:57374800-57409600	Weak transcription	Osteobl	bone
40	chr15:57374800-57414600	Weak transcription	Fetal Kidney	kidney
41	chr15:57375000-57385000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr15:57375000-57386200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:57375000-57386200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr15:57375000-57393400	Weak transcription	Fetal Intestine Small	intestine
45	chr15:57375000-57398000	Weak transcription	NH-A	brain
46	chr15:57375000-57398400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr15:57376200-57385800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr15:57376200-57406000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr15:57376600-57386200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr15:57376800-57382400	Weak transcription	Colon Smooth Muscle	Colon

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