Variant report

Variant	rs10810372
Chromosome Location	chr9:15292322-15292323
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	chr9:15283111..15284924-chr9:15291453..15293765,2	MCF-7	breast:
2	chr9:15290133..15292362-chr9:15306023..15308672,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155158	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10738391	0.88[CEU][hapmap];0.90[JPT][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10810368	1.00[ASW][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap]
rs10810373	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs10961959	0.92[CEU][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10961962	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11794919	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1215114	0.80[JPT][hapmap]
rs4741483	0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs570474	0.88[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs571888	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs585002	0.81[MKK][hapmap]
rs635376	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6474902	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][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	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2761505	chr9:15274373-15319613	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2762797	chr9:15282415-15297028	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv969751	chr9:15287487-15294727	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10810372	TTC39B	cis	lymphoblastoid	seeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15243000-15293400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr9:15254000-15293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:15254200-15293000	Weak transcription	NHEK	skin
4	chr9:15254200-15295600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:15259200-15293400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:15273600-15293400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:15277000-15293000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr9:15277600-15296800	Weak transcription	Gastric	stomach
9	chr9:15278000-15295200	Weak transcription	Pancreas	Pancrea
10	chr9:15279800-15293200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:15283600-15293800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr9:15285200-15293800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:15286800-15293200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:15286800-15293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:15287000-15293600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:15287000-15294200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr9:15287400-15303600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:15287600-15292800	Weak transcription	Primary T cells from cord blood	blood
19	chr9:15287600-15293000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:15287600-15293000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr9:15287600-15293600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr9:15287600-15294000	Weak transcription	Small Intestine	intestine
23	chr9:15288600-15293400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:15288600-15293400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:15288600-15294200	Weak transcription	HepG2	liver
26	chr9:15288800-15293800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:15288800-15293800	Weak transcription	Fetal Lung	lung
28	chr9:15288800-15294800	Weak transcription	Lung	lung
29	chr9:15289000-15293200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr9:15289000-15293400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:15289200-15293200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr9:15289200-15293400	Weak transcription	Esophagus	oesophagus
33	chr9:15289200-15295400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:15289400-15292400	Enhancers	Fetal Intestine Small	intestine
35	chr9:15289400-15292400	Enhancers	Fetal Stomach	stomach
36	chr9:15289400-15293400	Weak transcription	NHLF	lung
37	chr9:15290000-15293400	Weak transcription	Ovary	ovary
38	chr9:15290000-15293400	Weak transcription	HSMM	muscle
39	chr9:15290200-15292400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr9:15290600-15293200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr9:15290600-15293400	Weak transcription	Fetal Kidney	kidney
42	chr9:15290800-15293800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr9:15290800-15294200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr9:15290800-15305600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:15290800-15306000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:15291000-15293800	Weak transcription	Stomach Mucosa	stomach
47	chr9:15291200-15294200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:15291200-15296000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr9:15291200-15305600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr9:15291600-15294200	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links