Variant report

Variant	rs10934570
Chromosome Location	chr3:121718652-121718653
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10934568	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10934569	0.86[CHB][hapmap]
rs1143670	0.86[CHB][hapmap]
rs1143671	0.86[CHB][hapmap]
rs1143672	0.86[CHB][hapmap]
rs11718322	0.85[CHB][hapmap]
rs11914993	0.86[CHB][hapmap]
rs11920521	0.86[CHB][hapmap]
rs12637573	0.83[EUR][1000 genomes]
rs13074085	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1316397	0.86[CHB][hapmap]
rs1357531	0.86[CHB][hapmap]
rs1523517	0.86[CHB][hapmap]
rs1920289	0.86[EUR][1000 genomes]
rs1920319	0.86[CHB][hapmap]
rs2001212	1.00[CHB][hapmap]
rs2049330	0.86[CHB][hapmap]
rs2049331	0.86[CHB][hapmap]
rs2141615	0.80[CHB][hapmap]
rs2257115	0.86[CHB][hapmap]
rs2257119	0.86[CHB][hapmap]
rs2257132	0.86[CHB][hapmap]
rs2257212	0.86[CHB][hapmap]
rs2257214	0.86[CHB][hapmap]
rs2293614	0.86[CHB][hapmap]
rs2293616	0.86[CHB][hapmap]
rs2332034	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2332036	0.86[CHB][hapmap]
rs2332046	0.86[CHB][hapmap]
rs2689283	0.86[CHB][hapmap]
rs2700420	0.86[CHB][hapmap]
rs2700421	0.86[CHB][hapmap]
rs2877566	0.86[CHB][hapmap]
rs2877568	0.80[CHB][hapmap]
rs3762819	0.86[CHB][hapmap]
rs3762821	0.85[CHB][hapmap]
rs3805134	0.80[CHB][hapmap]
rs3805138	0.86[CHB][hapmap]
rs4325959	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438687	0.80[CHB][hapmap]
rs6793566	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6793858	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6803757	0.80[CHB][hapmap]
rs7637569	0.86[CHB][hapmap]
rs866927	0.80[CHB][hapmap]
rs874741	0.86[CHB][hapmap]
rs874742	0.86[CHB][hapmap]
rs9289182	0.80[CHB][hapmap]
rs9289183	0.80[CHB][hapmap]
rs9811389	0.86[EUR][1000 genomes]
rs9812515	0.86[CHB][hapmap]
rs9812869	0.86[EUR][1000 genomes]
rs9816720	0.93[CHB][hapmap]
rs9824120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825193	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9844039	0.86[EUR][1000 genomes]
rs9862977	0.86[CHB][hapmap]
rs9863154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868257	0.86[CHB][hapmap]
rs9871743	0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10934570	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121704800-121721400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:121705200-121729400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:121706000-121721200	Weak transcription	Fetal Kidney	kidney
4	chr3:121709200-121719200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:121709600-121721800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:121712200-121718800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:121712800-121721600	Weak transcription	Colonic Mucosa	Colon
8	chr3:121713000-121732200	Weak transcription	Esophagus	oesophagus
9	chr3:121713200-121719000	Enhancers	HUVEC	blood vessel
10	chr3:121713400-121718800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr3:121714400-121719800	Weak transcription	Lung	lung
12	chr3:121714600-121719200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:121714800-121719400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:121714800-121719600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:121714800-121720000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:121715000-121719400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:121715000-121719600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:121715400-121723400	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:121715400-121723400	Weak transcription	Fetal Thymus	thymus
20	chr3:121716200-121718800	Enhancers	Primary hematopoietic stem cells	blood
21	chr3:121716200-121720800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr3:121716600-121719800	Weak transcription	Pancreas	Pancrea
23	chr3:121716600-121720000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:121717200-121721600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:121717600-121720000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:121717600-121721200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr3:121717600-121721800	Weak transcription	HMEC	breast
28	chr3:121717800-121718800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:121717800-121718800	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr3:121717800-121719800	Weak transcription	Spleen	Spleen
31	chr3:121717800-121722200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:121718000-121719200	Weak transcription	Fetal Intestine Small	intestine
33	chr3:121718000-121720000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:121718000-121720600	Weak transcription	Fetal Intestine Large	intestine
35	chr3:121718000-121721600	Genic enhancers	GM12878-XiMat	blood
36	chr3:121718200-121718800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:121718200-121720800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr3:121718400-121718800	Enhancers	NHEK	skin
39	chr3:121718400-121719000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:121718400-121719800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:121718400-121721000	Weak transcription	Primary B cells from cord blood	blood
42	chr3:121718600-121718800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:121718600-121718800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:121718600-121718800	Enhancers	Hela-S3	cervix
45	chr3:121718600-121721400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:121718600-121721800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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