Variant report

Variant	rs9375789
Chromosome Location	chr6:131302731-131302732
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:131302451-131302918	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131301483..131303877-chr6:131310985..131313836,2	MCF-7	breast:

Variant related genes	Relation type
EPB41L2	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10457562	1.00[ASW][hapmap]
rs10457563	1.00[ASW][hapmap]
rs10872375	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11154611	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11760051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12193574	0.86[CHD][hapmap]
rs12195366	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196734	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12197829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12203760	0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12214021	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1569195	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs17059954	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1976981	0.84[ASN][1000 genomes]
rs2068147	0.82[CHD][hapmap]
rs2151068	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2178282	0.85[ASN][1000 genomes]
rs28812545	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777440	0.83[CHD][hapmap]
rs3777442	0.82[CHD][hapmap]
rs3777461	0.83[CHD][hapmap]
rs3777466	0.82[CHD][hapmap]
rs3822863	0.83[CHD][hapmap]
rs4259270	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4498389	0.91[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs62423583	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6901548	0.85[ASN][1000 genomes]
rs6902930	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6903705	0.85[ASN][1000 genomes]
rs6905151	0.80[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs6907809	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs6916206	0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs6921207	0.86[CHD][hapmap]
rs6921542	0.85[ASN][1000 genomes]
rs6926372	0.85[ASN][1000 genomes]
rs7763960	0.84[ASN][1000 genomes]
rs7770892	0.91[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9321264	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9372987	0.93[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9372989	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9375776	0.86[JPT][hapmap]
rs9375784	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9375785	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9375787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9375788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9375790	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9375794	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs9375795	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9375796	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9375797	0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs9385567	1.00[ASW][hapmap]
rs9388855	0.86[JPT][hapmap]
rs9388860	1.00[ASW][hapmap]
rs9388873	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9388876	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9388880	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9398967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9398969	0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9398970	0.85[ASN][1000 genomes]
rs9398971	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9398972	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9398973	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9398975	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9398976	0.85[EUR][1000 genomes]
rs9402287	0.86[JPT][hapmap]
rs9402299	0.83[CHD][hapmap]
rs9402301	0.94[ASN][1000 genomes]
rs9402306	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9402310	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9402313	0.85[ASN][1000 genomes]
rs9402314	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9483210	0.91[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9492790	0.81[ASN][1000 genomes]
rs9492792	0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs951251	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs954919	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9375789	CTGF	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131288200-131306600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:131291800-131306200	Weak transcription	Fetal Intestine Small	intestine
3	chr6:131292400-131306400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:131297600-131302800	Enhancers	Brain Cingulate Gyrus	brain
5	chr6:131298800-131314800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:131299000-131306200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:131299000-131309800	Weak transcription	HepG2	liver
8	chr6:131299200-131304600	Enhancers	Fetal Lung	lung
9	chr6:131299400-131303600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:131300200-131304000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:131300400-131312200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:131300400-131314600	Weak transcription	Small Intestine	intestine
13	chr6:131300800-131303800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:131301000-131305000	Enhancers	Dnd41	blood
15	chr6:131301200-131304600	Enhancers	Fetal Kidney	kidney
16	chr6:131301400-131302800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr6:131301400-131303000	Enhancers	Primary T cells from cord blood	blood
18	chr6:131301400-131303400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:131301800-131305000	Enhancers	Colon Smooth Muscle	Colon
20	chr6:131301800-131306200	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:131302000-131302800	Enhancers	NHLF	lung
22	chr6:131302000-131303400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:131302000-131304000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:131302200-131302800	Enhancers	HSMM	muscle
25	chr6:131302200-131303400	Enhancers	Brain Germinal Matrix	brain
26	chr6:131302200-131304000	Weak transcription	K562	blood
27	chr6:131302200-131304400	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr6:131302400-131302800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:131302400-131303600	Enhancers	NHDF-Ad	bronchial
30	chr6:131302400-131304200	Enhancers	Adipose Nuclei	Adipose
31	chr6:131302400-131304800	Enhancers	Rectal Smooth Muscle	rectum
32	chr6:131302400-131306400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:131302600-131302800	Enhancers	Primary B cells from peripheral blood	blood
34	chr6:131302600-131302800	Enhancers	Brain Angular Gyrus	brain
35	chr6:131302600-131302800	Enhancers	Brain Hippocampus Middle	brain
36	chr6:131302600-131302800	Enhancers	Thymus	Thymus
37	chr6:131302600-131303000	Enhancers	Brain Substantia Nigra	brain
38	chr6:131302600-131303000	Enhancers	GM12878-XiMat	blood
39	chr6:131302600-131303400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:131302600-131303600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr6:131302600-131304000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:131302600-131304000	Weak transcription	Fetal Stomach	stomach
43	chr6:131302600-131304200	Enhancers	Brain Anterior Caudate	brain

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