Variant report

Variant	rs10117638
Chromosome Location	chr9:102687082-102687083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:102679510..102681495-chr9:102684223..102687108,2	K562	blood:
2	chr9:102685655..102688610-chr9:102689840..102691723,2	MCF-7	breast:
3	chr9:102681063..102683683-chr9:102683801..102687863,4	MCF-7	breast:
4	chr9:102679685..102682942-chr9:102684269..102688000,3	K562	blood:

Variant related genes	Relation type
ENSG00000136874	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10116142	0.83[JPT][hapmap]
rs10117828	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10120103	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10121601	0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs10121880	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10122128	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123261	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10124366	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs10125981	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217337	0.94[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs10217366	0.93[ASN][1000 genomes]
rs10217692	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10512268	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs1055187	0.88[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10739791	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739793	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760698	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760700	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10760704	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs10760705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760706	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10819705	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819706	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819707	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819711	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988919	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988920	0.92[ASN][1000 genomes]
rs12352899	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830454	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs1852863	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs1881751	0.90[ASN][1000 genomes]
rs1962051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997367	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs1997368	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2031035	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs2416935	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2416936	0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2416937	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2416938	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2416940	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2416941	0.93[ASN][1000 genomes]
rs2416942	0.93[ASN][1000 genomes]
rs2900224	0.92[ASN][1000 genomes]
rs3739794	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3983846	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4282626	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4452862	0.93[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs4585797	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4742777	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4742778	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743370	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs6478987	0.93[ASN][1000 genomes]
rs6478988	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478990	0.93[ASN][1000 genomes]
rs7022208	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022999	0.93[ASN][1000 genomes]
rs7027619	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7027813	0.95[ASN][1000 genomes]
rs7030388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038506	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7039716	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7853264	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299335	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs9556	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv1050510	chr9:102684318-102748658	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10117638	STX17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102669800-102687600	Weak transcription	Stomach Mucosa	stomach
2	chr9:102669800-102729800	Weak transcription	Small Intestine	intestine
3	chr9:102670000-102688200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:102670400-102688600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr9:102671200-102719200	Weak transcription	Fetal Heart	heart
6	chr9:102676600-102688000	Strong transcription	Primary B cells from cord blood	blood
7	chr9:102677600-102687200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr9:102677600-102687800	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:102677800-102687200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr9:102677800-102687400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:102680000-102710800	Weak transcription	HUVEC	blood vessel
12	chr9:102680400-102693800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:102680400-102724800	Weak transcription	HSMM	muscle
14	chr9:102680600-102689000	Weak transcription	Fetal Brain Male	brain
15	chr9:102681800-102690400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:102682600-102693800	Weak transcription	Osteobl	bone
17	chr9:102682600-102751400	Weak transcription	NH-A	brain
18	chr9:102682800-102687800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr9:102682800-102695000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:102683000-102687600	Weak transcription	Brain Germinal Matrix	brain
21	chr9:102683400-102687200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr9:102683600-102687800	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr9:102684000-102687600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr9:102684200-102687200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr9:102684200-102687200	Strong transcription	A549	lung
26	chr9:102684200-102687800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:102684200-102689400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:102684400-102691400	Weak transcription	NHDF-Ad	bronchial
29	chr9:102684400-102720600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr9:102684600-102688200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:102684600-102693600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:102684800-102687600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr9:102684800-102687800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:102684800-102689800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:102685000-102687800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr9:102685000-102690800	Weak transcription	HSMMtube	muscle
37	chr9:102685000-102698200	Weak transcription	NHEK	skin
38	chr9:102685000-102710000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr9:102685000-102731600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr9:102685200-102687600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr9:102685200-102730200	Weak transcription	NHLF	lung
42	chr9:102685400-102687600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr9:102685400-102690800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr9:102685800-102689400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr9:102685800-102691000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:102685800-102698000	Weak transcription	HMEC	breast
47	chr9:102686000-102688800	Weak transcription	Left Ventricle	heart
48	chr9:102686000-102695400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr9:102686000-102699400	Weak transcription	K562	blood
50	chr9:102686200-102687400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links