Variant report

Variant	rs12685807
Chromosome Location	chr9:98645426-98645427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98644374..98646998-chr9:98660119..98662324,2	MCF-7	breast:
2	chr9:98643243..98646230-chr9:98646548..98650436,4	MCF-7	breast:
3	chr9:98642876..98646721-chr9:98647995..98651810,4	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10759883	0.91[YRI][hapmap]
rs10988792	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10988804	0.89[GIH][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap]
rs11787559	0.82[EUR][1000 genomes]
rs12001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12683310	0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12685221	0.82[EUR][1000 genomes]
rs12685318	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1360064	0.89[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs16910262	0.90[AFR][1000 genomes]
rs16910296	0.92[ASW][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs16910298	0.92[ASW][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1831228	0.82[EUR][1000 genomes]
rs1999023	0.89[GIH][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap]
rs2069053	0.92[GIH][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs2274653	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274654	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3802438	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4742775	0.89[GIH][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap]
rs4742781	0.92[GIH][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs4743372	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs4743391	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743400	0.93[CHB][hapmap];0.83[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743417	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743419	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7048414	0.86[GIH][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap]
rs7868270	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[EUR][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12685807	C9orf130	cis	parietal	SCAN
rs12685807	C9orf130	cis	lesional skin	skin_eQTL
rs12685807	HABP4	cis	cerebellum	SCAN
rs12685807	OGN	cis	parietal	SCAN
rs12685807	AUH	cis	parietal	SCAN
rs12685807	LINC00476	cis	Esophagus Mucosa	GTEx
rs12685807	LINC00476	cis	Whole Blood	GTEx
rs12685807	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs12685807	LINC00476	cis	Adipose Subcutaneous	GTEx
rs12685807	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx
rs12685807	LINC00476	cis	Esophagus Muscularis	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98648000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:98638800-98648400	Weak transcription	Lung	lung
3	chr9:98638800-98649000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:98638800-98654800	Weak transcription	Esophagus	oesophagus
5	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
6	chr9:98639400-98647800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:98639400-98649000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:98639400-98650800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:98639400-98677800	Weak transcription	Placenta	Placenta
10	chr9:98639400-98678000	Weak transcription	Ovary	ovary
11	chr9:98639600-98646200	Weak transcription	HSMMtube	muscle
12	chr9:98639600-98649200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:98639600-98678000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:98639800-98664200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:98639800-98677800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:98640000-98649000	Weak transcription	Spleen	Spleen
17	chr9:98640000-98661600	Weak transcription	Right Atrium	heart
18	chr9:98640000-98663600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:98640000-98678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:98640000-98680600	Weak transcription	Colonic Mucosa	Colon
21	chr9:98640000-98685600	Weak transcription	Right Ventricle	heart
22	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr9:98640200-98678200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:98640400-98649200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr9:98640400-98664800	Weak transcription	Brain Substantia Nigra	brain
26	chr9:98640400-98677800	Weak transcription	Psoas Muscle	Psoas
27	chr9:98640600-98647800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr9:98640600-98649000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:98640600-98678000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr9:98641400-98646400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr9:98641600-98650000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr9:98642000-98647200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:98642000-98647600	Weak transcription	Fetal Brain Male	brain
34	chr9:98642200-98647600	Weak transcription	Fetal Heart	heart
35	chr9:98642200-98652400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr9:98642200-98654600	Weak transcription	Fetal Intestine Small	intestine
37	chr9:98642200-98663600	Weak transcription	Hela-S3	cervix
38	chr9:98642600-98678000	Weak transcription	Colon Smooth Muscle	Colon
39	chr9:98642600-98680600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr9:98642800-98668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:98642800-98681800	Weak transcription	Fetal Kidney	kidney
42	chr9:98643000-98645800	Weak transcription	NH-A	brain
43	chr9:98643000-98648400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:98643200-98645800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr9:98643200-98647800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr9:98643200-98648200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr9:98643200-98648400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr9:98643200-98649000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:98643200-98649800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr9:98643200-98651200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links