Variant report

Variant	rs9372987
Chromosome Location	chr6:131360522-131360523
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131356533..131360824-chr6:131360872..131363958,3	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10872375	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11154611	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11760051	0.93[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12195366	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12196734	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12197829	0.93[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12203760	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12214021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1569195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17059954	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1976981	0.98[ASN][1000 genomes]
rs2151068	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178282	0.99[ASN][1000 genomes]
rs28812545	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259270	0.89[CEU][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]
rs4498389	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs543363	1.00[ASW][hapmap]
rs62423583	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs677072	1.00[ASW][hapmap]
rs6901548	0.97[ASN][1000 genomes]
rs6902930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903705	0.99[ASN][1000 genomes]
rs6905151	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs6907809	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6916206	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6921542	0.99[ASN][1000 genomes]
rs6926372	0.97[ASN][1000 genomes]
rs7763960	0.98[ASN][1000 genomes]
rs7770892	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9321264	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9372986	0.91[ASN][1000 genomes]
rs9372989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9375784	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9375785	0.80[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375787	0.93[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9375788	0.93[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9375789	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]
rs9375790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9375794	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9375795	0.91[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9375796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375797	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs9388873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9388876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388880	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9398967	0.93[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398969	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398970	0.99[ASN][1000 genomes]
rs9398971	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9398972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398973	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398975	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9398976	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9402301	0.85[ASN][1000 genomes]
rs9402306	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9402310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9402313	0.99[ASN][1000 genomes]
rs9402314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9483210	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9492790	0.95[ASN][1000 genomes]
rs9492792	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs951251	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs954919	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[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
rs9372987	CTGF	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131346000-131375000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:131351400-131361400	Weak transcription	Psoas Muscle	Psoas
3	chr6:131351400-131375000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:131351600-131374600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:131352400-131374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:131353800-131364000	Weak transcription	Ovary	ovary
7	chr6:131356600-131375000	Weak transcription	Brain Angular Gyrus	brain
8	chr6:131357400-131367200	Weak transcription	Fetal Intestine Small	intestine
9	chr6:131358600-131360800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:131359000-131374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:131359200-131360600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:131359400-131360800	Enhancers	Fetal Lung	lung
13	chr6:131359400-131360800	Enhancers	HSMM	muscle
14	chr6:131359600-131360600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:131359600-131360800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:131359800-131360600	Enhancers	Brain Hippocampus Middle	brain
17	chr6:131359800-131360800	Enhancers	Liver	Liver
18	chr6:131359800-131360800	Enhancers	Brain Anterior Caudate	brain
19	chr6:131359800-131360800	Enhancers	Brain Cingulate Gyrus	brain
20	chr6:131359800-131360800	Enhancers	Fetal Kidney	kidney
21	chr6:131359800-131361000	Enhancers	Brain Substantia Nigra	brain
22	chr6:131359800-131361000	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr6:131359800-131361200	Enhancers	Colon Smooth Muscle	Colon
24	chr6:131360000-131360600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr6:131360000-131360600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr6:131360000-131360600	Enhancers	A549	lung
27	chr6:131360000-131360600	Flanking Active TSS	Osteobl	bone
28	chr6:131360000-131360800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:131360000-131360800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr6:131360000-131360800	Enhancers	HSMMtube	muscle
31	chr6:131360000-131360800	Flanking Active TSS	NHDF-Ad	bronchial
32	chr6:131360000-131360800	Flanking Active TSS	NHLF	lung
33	chr6:131360200-131360600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr6:131360200-131360600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:131360200-131360800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:131360200-131360800	Enhancers	Small Intestine	intestine
37	chr6:131360200-131360800	Enhancers	HUVEC	blood vessel
38	chr6:131360200-131361400	Enhancers	Fetal Muscle Leg	muscle
39	chr6:131360200-131361400	Enhancers	Fetal Stomach	stomach
40	chr6:131360400-131360800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:131360400-131360800	Flanking Active TSS	HepG2	liver
42	chr6:131360400-131365600	Weak transcription	Adipose Nuclei	Adipose
43	chr6:131360400-131367400	Weak transcription	Brain Inferior Temporal Lobe	brain

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