Variant report

Variant	rs17415731
Chromosome Location	chr15:57270286-57270287
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	chr15:57269633..57272065-chr15:57273062..57274627,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10467927	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10851612	0.91[CHB][hapmap]
rs11071303	0.82[ASN][1000 genomes]
rs11071308	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1115019	0.86[CHB][hapmap]
rs11856338	0.83[AFR][1000 genomes]
rs11856411	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13379847	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1430820	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1430822	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1441236	0.86[CHB][hapmap]
rs1657922	0.86[CHB][hapmap]
rs16977153	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16977222	0.82[ASN][1000 genomes]
rs16977243	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs16977270	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1820994	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2169467	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2278613	0.91[CHB][hapmap]
rs2593211	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2593249	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2593252	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2703614	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2733333	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2733334	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs28360967	0.97[ASN][1000 genomes]
rs28612876	0.96[ASN][1000 genomes]
rs28648577	0.97[ASN][1000 genomes]
rs28649108	0.97[ASN][1000 genomes]
rs28654848	0.97[ASN][1000 genomes]
rs28677775	0.97[ASN][1000 genomes]
rs28756149	0.95[ASN][1000 genomes]
rs28814080	0.88[ASN][1000 genomes]
rs4774245	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6493900	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7162194	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7163267	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7164655	0.87[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7171073	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7171304	0.90[CEU][hapmap];0.80[ASN][1000 genomes]
rs7175191	0.91[CHB][hapmap]
rs7176873	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7178833	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs8023343	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8023816	0.97[ASN][1000 genomes]
rs8031516	0.95[ASN][1000 genomes]
rs8031640	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs8032615	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs8033010	0.90[ASN][1000 genomes]
rs8034066	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs8034502	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs8035485	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8035916	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs8039899	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9302200	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs9806170	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs9806199	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]

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	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	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
3	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
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17415731	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57256800-57277200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:57257200-57274600	Weak transcription	Adipose Nuclei	Adipose
3	chr15:57260000-57272200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:57260000-57272400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:57261200-57272800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr15:57261200-57279000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:57261400-57272000	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:57261400-57275000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:57262200-57270800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:57262200-57280000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:57263800-57271000	Weak transcription	Hela-S3	cervix
12	chr15:57263800-57272400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr15:57263800-57276000	Weak transcription	Lung	lung
14	chr15:57264200-57270600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:57264200-57270800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:57264200-57272600	Weak transcription	Thymus	Thymus
17	chr15:57264200-57272800	Weak transcription	Right Atrium	heart
18	chr15:57264200-57272800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:57264800-57275000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:57264800-57275200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr15:57265000-57272800	Weak transcription	Brain Angular Gyrus	brain
22	chr15:57265400-57277000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:57265600-57270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:57265600-57271200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:57265800-57271000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:57265800-57271000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:57266200-57270800	Weak transcription	NHLF	lung
28	chr15:57266200-57271000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:57266200-57271000	Weak transcription	NHDF-Ad	bronchial
30	chr15:57266200-57271600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:57266200-57272000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr15:57266200-57272200	Weak transcription	Small Intestine	intestine
33	chr15:57266200-57274200	Weak transcription	Liver	Liver
34	chr15:57266400-57270800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:57266400-57271000	Weak transcription	K562	blood
36	chr15:57266400-57272800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr15:57266600-57270800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:57266600-57271200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:57266600-57272800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:57267000-57270800	Weak transcription	Primary T cells from cord blood	blood
41	chr15:57267000-57273200	Weak transcription	Dnd41	blood
42	chr15:57267000-57273400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:57267000-57274600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:57267400-57274000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:57267800-57271600	Weak transcription	HSMM	muscle
46	chr15:57268200-57270800	Weak transcription	HepG2	liver
47	chr15:57268200-57271000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr15:57268800-57270400	Strong transcription	Fetal Thymus	thymus
49	chr15:57269400-57270800	Enhancers	A549	lung
50	chr15:57269600-57270400	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links