Variant report

Variant	rs12347675
Chromosome Location	chr9:98635343-98635344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98614433..98624477-chr9:98629889..98639636,23	MCF-7	breast:
2	chr9:98624670..98626766-chr9:98633478..98635523,2	K562	blood:

Variant related genes	Relation type
ENSG00000252847	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10115110	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10117340	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10125109	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10512242	0.81[AMR][1000 genomes]
rs10512245	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10739622	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739705	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10760189	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10760261	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760262	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760269	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760679	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10818574	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10818746	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10818899	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819650	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10819663	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10819668	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10819720	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10985156	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10985499	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10985769	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10987963	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10988755	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10988817	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10989035	0.85[AMR][1000 genomes]
rs1195130	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11998982	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12000073	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12340954	0.86[AMR][1000 genomes]
rs12343734	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12345187	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12348051	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12349742	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1327996	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1327997	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13289466	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13294931	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13298093	0.81[AMR][1000 genomes]
rs13299166	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2026031	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296858	0.90[AMR][1000 genomes]
rs2405134	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2405371	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2405372	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2943532	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs589362	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs596413	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603947	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs609296	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs617187	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs623438	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs624075	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs625105	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62559026	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62559767	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs640297	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6478977	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs649819	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs657451	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs666093	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs667705	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs671058	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs682682	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs684455	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs686048	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs689619	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs689696	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs689697	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689710	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs689738	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs689744	0.90[AMR][1000 genomes]
rs689761	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs689804	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689860	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs689911	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689986	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690056	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs690063	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs690286	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs690495	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs690528	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690633	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs694230	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs700962	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7847393	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7847983	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7852346	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7871709	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816670	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816672	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816673	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816674	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816675	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816678	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs816680	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816682	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs816683	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816684	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs966217	0.96[AMR][1000 genomes];0.93[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12347675	ERCC6L2	cis	Artery Tibial	GTEx
rs12347675	ERCC6L2	cis	Adipose Subcutaneous	GTEx
rs12347675	C9orf130	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98602000-98636000	Weak transcription	Lung	lung
2	chr9:98610200-98636200	Weak transcription	Brain Germinal Matrix	brain
3	chr9:98610200-98636800	Weak transcription	Gastric	stomach
4	chr9:98620400-98636200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:98620600-98636600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:98621000-98636400	Weak transcription	Hela-S3	cervix
7	chr9:98624600-98636400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:98625000-98636200	Weak transcription	Fetal Lung	lung
9	chr9:98626200-98636400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:98628000-98636400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:98628200-98636200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:98628400-98636800	Weak transcription	Thymus	Thymus
13	chr9:98629200-98636600	Weak transcription	Primary B cells from cord blood	blood
14	chr9:98630200-98636200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:98630400-98636600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:98630600-98636200	Weak transcription	Brain Anterior Caudate	brain
17	chr9:98630600-98636400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:98631200-98636000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:98631200-98636600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:98631200-98636600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr9:98631200-98636600	Weak transcription	NH-A	brain
22	chr9:98631400-98636400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:98631400-98636600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:98631400-98636600	Weak transcription	Osteobl	bone
25	chr9:98631800-98636400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:98631800-98636400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr9:98631800-98636800	Weak transcription	Ovary	ovary
28	chr9:98632000-98636800	Weak transcription	Esophagus	oesophagus
29	chr9:98632200-98636400	Weak transcription	Fetal Intestine Small	intestine
30	chr9:98632200-98636600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:98632400-98636800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr9:98632600-98636000	Weak transcription	Brain Hippocampus Middle	brain
33	chr9:98632600-98636600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:98632800-98635400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:98632800-98636400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:98632800-98636800	Weak transcription	Placenta	Placenta
37	chr9:98632800-98636800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr9:98633000-98636000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr9:98633000-98636600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:98633000-98636800	Weak transcription	HSMMtube	muscle
41	chr9:98633200-98635800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr9:98633200-98636200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr9:98633200-98636400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr9:98633200-98636400	Weak transcription	HMEC	breast
45	chr9:98633200-98636600	Weak transcription	Adipose Nuclei	Adipose
46	chr9:98633200-98636800	Weak transcription	Fetal Thymus	thymus
47	chr9:98633400-98636400	Weak transcription	Colonic Mucosa	Colon
48	chr9:98633400-98636400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr9:98633400-98636600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr9:98633400-98636600	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links