Variant report

Variant	rs10739632
Chromosome Location	chr9:98616743-98616744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98614433..98624477-chr9:98629889..98639636,23	MCF-7	breast:
2	chr9:98611900..98615420-chr9:98615884..98619826,3	MCF-7	breast:
3	chr9:98610483..98612761-chr9:98615840..98617513,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10121403	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10481647	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760675	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760692	0.88[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes]
rs10818017	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10983622	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10983692	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10983739	0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10983773	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10983818	0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12004422	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375861	0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12553442	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1410783	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1928253	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2117432	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2164156	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2164157	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs238	0.82[GIH][hapmap];0.83[TSI][hapmap]
rs2770837	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3930253	0.84[AMR][1000 genomes]
rs4743458	0.80[AMR][1000 genomes]
rs583716	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs585223	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs591579	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs601916	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs615866	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs617884	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs626264	0.88[AMR][1000 genomes]
rs631273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs636456	0.87[AMR][1000 genomes]
rs643815	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478984	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6479036	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs676453	0.84[AMR][1000 genomes]
rs680468	0.87[GIH][hapmap];0.84[AMR][1000 genomes]
rs680754	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs683829	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs689627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs689749	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689820	0.88[AMR][1000 genomes]
rs689871	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689979	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs690222	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690304	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690335	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690420	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs690455	0.88[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes]
rs690484	0.88[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes]
rs700963	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7024710	0.88[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes]
rs7028281	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7868559	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7874897	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816671	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs816676	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs816681	0.86[ASN][1000 genomes]
rs913408	0.88[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes]
rs9409321	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9409322	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10739632	LINC00476	cis	Nerve Tibial	GTEx
rs10739632	HSD17B3	cis	parietal	SCAN
rs10739632	C9orf130	cis	cerebellum	SCAN
rs10739632	LINC00476	cis	Thyroid	GTEx
rs10739632	FGD3	cis	parietal	SCAN
rs10739632	LINC00476	cis	Artery Aorta	GTEx
rs10739632	C9orf130	cis	parietal	SCAN
rs10739632	LINC00476	cis	Adipose Subcutaneous	GTEx
rs10739632	LINC00476	cis	lung	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98596200-98619200	Weak transcription	Fetal Heart	heart
2	chr9:98596400-98619400	Weak transcription	Right Ventricle	heart
3	chr9:98602000-98632800	Weak transcription	Left Ventricle	heart
4	chr9:98602000-98636000	Weak transcription	Lung	lung
5	chr9:98602400-98619400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:98602600-98618800	Weak transcription	Fetal Muscle Leg	muscle
7	chr9:98602600-98619400	Weak transcription	Psoas Muscle	Psoas
8	chr9:98602600-98620200	Weak transcription	Small Intestine	intestine
9	chr9:98602800-98619000	Weak transcription	Ovary	ovary
10	chr9:98604400-98621200	Weak transcription	Primary T cells from cord blood	blood
11	chr9:98607400-98621600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr9:98609000-98617200	Weak transcription	Spleen	Spleen
13	chr9:98609000-98619400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:98610200-98636200	Weak transcription	Brain Germinal Matrix	brain
15	chr9:98610200-98636800	Weak transcription	Gastric	stomach
16	chr9:98610400-98618800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:98610600-98618200	Weak transcription	Thymus	Thymus
18	chr9:98610600-98618800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:98610600-98619400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:98611200-98620200	Weak transcription	Primary B cells from cord blood	blood
21	chr9:98611200-98620400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:98611400-98619200	Weak transcription	Fetal Intestine Small	intestine
23	chr9:98613400-98632800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr9:98614000-98616800	Enhancers	HUVEC	blood vessel
25	chr9:98614200-98618200	Enhancers	NHLF	lung
26	chr9:98614200-98620400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:98614400-98617400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:98614400-98617600	Enhancers	HMEC	breast
29	chr9:98614400-98620200	Enhancers	NHEK	skin
30	chr9:98614600-98620000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr9:98615000-98619400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:98615200-98620400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr9:98615200-98624400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:98615400-98616800	Weak transcription	Osteobl	bone
35	chr9:98615400-98617000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:98615400-98619200	Weak transcription	HSMMtube	muscle
37	chr9:98615400-98619400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:98615400-98624000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:98615600-98616800	Weak transcription	Hela-S3	cervix
40	chr9:98615600-98618200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:98615600-98619400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:98615800-98616800	Weak transcription	NH-A	brain
43	chr9:98615800-98617200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:98615800-98618400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr9:98615800-98618800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr9:98615800-98619400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr9:98615800-98619400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:98615800-98620200	Weak transcription	K562	blood
49	chr9:98616000-98620600	Enhancers	Fetal Lung	lung
50	chr9:98616200-98617000	Active TSS	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links