Variant report

Variant	rs17215862
Chromosome Location	chr4:104027644-104027645
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	chr4:104020991..104023590-chr4:104027343..104030136,2	K562	blood:

Variant related genes	Relation type
ENSG00000164039	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10516498	0.89[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054707	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11724466	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724522	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725048	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11727029	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11729856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11730764	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730765	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734318	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11737673	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12500951	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504143	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12504262	0.89[CHB][hapmap];0.94[ASN][1000 genomes]
rs12505289	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505908	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506065	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506157	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507348	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508269	0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs12511516	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12512468	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1381657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1381658	0.93[CEU][hapmap];0.87[CHB][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17215694	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17215785	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217431	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17217592	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17283027	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17283077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17283194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17522932	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306478	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2720469	0.94[CHD][hapmap]
rs2866633	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35714833	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765086	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775972	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.99[ASN][1000 genomes]
rs3796982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796983	0.89[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs3974474	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55895342	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56126326	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56256243	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56378042	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56412006	0.94[ASN][1000 genomes]
rs58648171	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58888668	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59192877	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59341670	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61355145	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533057	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66869812	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6822891	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6825519	0.89[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6830791	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836162	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837114	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6840401	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665040	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665042	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665048	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665052	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665054	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665056	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665063	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72665071	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72665093	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72665096	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72666812	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs736048	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746829	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662455	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7664021	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7666067	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs7668568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675057	0.94[CHD][hapmap];0.93[ASN][1000 genomes]
rs7686105	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7690059	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers 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 miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17215862	BDH2	cis	Esophagus Muscularis	GTEx
rs17215862	BDH2	cis	Thyroid	GTEx
rs17215862	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs17215862	BDH2	cis	lung	GTEx
rs17215862	BDH2	cis	cerebellum	SCAN
rs17215862	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs17215862	BDH2	cis	Artery Tibial	GTEx
rs17215862	PPP3CA	cis	parietal	SCAN
rs17215862	BDH2	cis	Nerve Tibial	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104012400-104028200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:104019800-104030200	Weak transcription	Esophagus	oesophagus
3	chr4:104021000-104028000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:104021000-104028200	Weak transcription	Brain Germinal Matrix	brain
5	chr4:104021000-104028600	Weak transcription	HSMM	muscle
6	chr4:104021000-104029800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:104021000-104031600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:104021000-104031600	Weak transcription	Placenta	Placenta
9	chr4:104021000-104033600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:104021000-104049200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:104021000-104049200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:104021000-104056000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:104021000-104058200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:104021000-104063800	Weak transcription	Fetal Stomach	stomach
15	chr4:104021000-104068400	Weak transcription	Fetal Brain Male	brain
16	chr4:104021000-104076400	Weak transcription	Fetal Brain Female	brain
17	chr4:104021000-104089600	Weak transcription	Fetal Heart	heart
18	chr4:104021200-104027800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:104021200-104028200	Weak transcription	Primary B cells from cord blood	blood
20	chr4:104021200-104028600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:104021200-104028600	Weak transcription	NHDF-Ad	bronchial
22	chr4:104021200-104028800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:104021200-104028800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr4:104021200-104029800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:104021200-104030200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:104021200-104030400	Weak transcription	Primary T cells from cord blood	blood
27	chr4:104021200-104032400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:104021200-104032600	Weak transcription	Fetal Kidney	kidney
29	chr4:104021200-104032800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:104021200-104045800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:104021200-104076600	Weak transcription	Fetal Intestine Small	intestine
32	chr4:104021200-104100200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr4:104021400-104028000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:104021400-104028000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:104021400-104028000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:104021400-104028000	Weak transcription	Hela-S3	cervix
37	chr4:104021400-104028200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr4:104021400-104028200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:104021400-104028200	Weak transcription	Fetal Lung	lung
40	chr4:104021400-104028400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:104021400-104028800	Weak transcription	NHLF	lung
42	chr4:104021400-104030600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr4:104021400-104030800	Weak transcription	A549	lung
44	chr4:104021400-104074600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:104022200-104028000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:104022200-104028200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:104026200-104031600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:104026200-104033200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:104026200-104033400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:104026400-104033000	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links