Variant report

Variant	rs9372989
Chromosome Location	chr6:131385042-131385043
allele	A/G
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	MAX	chr6:131383524-131385283	A549	lung:	n/a	chr6:131383712-131383721
2	ATF2	chr6:131384651-131385318	GM12878	blood:	n/a	n/a
3	EGR1	chr6:131384109-131385122	HCT-116	colon:	n/a	chr6:131384522-131384536 chr6:131384134-131384147 chr6:131384133-131384143
4	POLR2A	chr6:131384131-131385219	GM19193	blood:	n/a	n/a
5	PAX5	chr6:131384788-131385266	GM12878	blood:	n/a	chr6:131384961-131384988
6	SMC3	chr6:131384708-131385080	GM12878	blood:	n/a	n/a
7	GATA2	chr6:131384303-131385141	HUVEC	blood vessel:	n/a	n/a
8	RUNX3	chr6:131384198-131385284	GM12878	blood:	n/a	n/a
9	RCOR1	chr6:131384179-131385092	HepG2	liver:	n/a	n/a
10	NFIC	chr6:131384333-131385378	GM12878	blood:	n/a	n/a
11	MXI1	chr6:131384163-131385274	GM12878	blood:	n/a	n/a
12	RELA	chr6:131384175-131385192	GM15510	blood:	n/a	chr6:131384898-131384907 chr6:131384898-131384907
13	MAZ	chr6:131382443-131385497	IMR90	lung:	n/a	chr6:131383712-131383721
14	MAX	chr6:131384706-131385209	A549	lung:	n/a	n/a
15	TEAD4	chr6:131384096-131385080	HepG2	liver:	n/a	n/a
16	RELA	chr6:131384214-131385233	GM18951	blood:	n/a	chr6:131384898-131384907 chr6:131384898-131384907
17	FOS	chr6:131384456-131385092	HUVEC	blood vessel:	n/a	chr6:131384722-131384734
18	MAZ	chr6:131383386-131385101	HepG2	liver:	n/a	chr6:131383712-131383721
19	KAP1	chr6:131384490-131385299	U2OS	brain:	n/a	n/a
20	CREB1	chr6:131384003-131385315	HepG2	liver:	n/a	n/a
21	BCL3	chr6:131384847-131385229	GM12878	blood:	n/a	chr6:131384897-131384906 chr6:131384896-131384905
22	RCOR1	chr6:131384234-131385423	GM12878	blood:	n/a	n/a
23	SP1	chr6:131384800-131385339	GM12878	blood:	n/a	n/a
24	MAX	chr6:131384905-131385353	HepG2	liver:	n/a	n/a
25	FOXM1	chr6:131384674-131385357	GM12878	blood:	n/a	n/a
26	MTA3	chr6:131384496-131385231	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:131384135-131385235	HepG2	liver:	n/a	n/a
28	MYBL2	chr6:131384130-131385337	HepG2	liver:	n/a	n/a
29	MAZ	chr6:131383468-131385208	K562	blood:	n/a	chr6:131383712-131383721
30	KAP1	chr6:131384604-131385390	HEK293	kidney:	n/a	n/a
31	BCL11A	chr6:131384800-131385269	GM12878	blood:	n/a	chr6:131384897-131384906 chr6:131384896-131384905
32	WRNIP1	chr6:131384593-131385236	GM12878	blood:	n/a	n/a
33	ATF2	chr6:131384535-131385286	GM12878	blood:	n/a	n/a
34	RELA	chr6:131384239-131385226	GM12878	blood:	n/a	chr6:131384898-131384907 chr6:131384898-131384907
35	POLR2A	chr6:131384135-131385307	GM12878	blood:	n/a	n/a
36	BATF	chr6:131384817-131385312	GM12878	blood:	n/a	n/a
37	MAX	chr6:131383321-131385376	HepG2	liver:	n/a	chr6:131383712-131383721
38	MYC	chr6:131384228-131385133	K562	blood:	n/a	n/a
39	MAZ	chr6:131383400-131385207	GM12878	blood:	n/a	chr6:131383712-131383721
40	CHD1	chr6:131384649-131385217	GM12878	blood:	n/a	n/a
41	NRF1	chr6:131384332-131385043	GM12878	blood:	n/a	n/a
42	PAX5	chr6:131384858-131385272	GM12878	blood:	n/a	chr6:131384961-131384988
43	MXI1	chr6:131380933-131385493	IMR90	lung:	n/a	n/a
44	MEF2C	chr6:131384768-131385248	GM12878	blood:	n/a	n/a
45	TBL1XR1	chr6:131384235-131385305	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:131384104-131385271	GM12878	blood:	n/a	n/a
47	MXI1	chr6:131384090-131385221	HepG2	liver:	n/a	n/a
48	POLR2A	chr6:131383553-131385175	GM19099	blood:	n/a	n/a
49	CREB1	chr6:131384126-131385438	GM12878	blood:	n/a	n/a
50	EGR1	chr6:131384145-131385103	HCT-116	colon:	n/a	chr6:131384522-131384536

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131380112..131382721-chr6:131384592..131387517,3	K562	blood:
2	chr6:131383272..131386235-chr6:131948272..131950497,3	MCF-7	breast:

Variant related genes	Relation type
EPB41L2	TF binding region
ENSG00000112282	Chromatin interaction
ENSG00000154269	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10457562	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs10457563	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs10872375	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11154611	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11760051	0.93[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12195366	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12196734	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.82[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];0.80[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12203760	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12214021	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1569195	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs17059954	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1976981	0.96[ASN][1000 genomes]
rs2151068	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2178282	0.97[ASN][1000 genomes]
rs28812545	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4259270	0.89[CEU][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]
rs4498389	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs62423583	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6901548	0.99[ASN][1000 genomes]
rs6902930	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6903705	0.97[ASN][1000 genomes]
rs6905151	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs6907809	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6916206	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs6921542	0.97[ASN][1000 genomes]
rs6926372	0.99[ASN][1000 genomes]
rs7763960	0.99[ASN][1000 genomes]
rs7770892	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9321264	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9372986	0.89[ASN][1000 genomes]
rs9372987	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	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9375785	0.80[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9375787	0.93[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375788	0.93[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375789	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]
rs9375790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9375794	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs9375795	0.91[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9375796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9375797	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9388873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9388876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9388880	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9398967	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9398969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][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]
rs9398970	0.97[ASN][1000 genomes]
rs9398971	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9398972	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9398973	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9398975	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9398976	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9402301	0.84[ASN][1000 genomes]
rs9402306	0.91[CHB][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs9402310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9402313	0.97[ASN][1000 genomes]
rs9402314	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9483210	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs9492790	0.93[ASN][1000 genomes]
rs9492792	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs951251	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs954919	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3370421	chr6:131383359-131385457	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9372989	CTGF	cis	parietal	SCAN
rs9372989	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131381800-131385200	Active TSS	Brain Anterior Caudate	brain
2	chr6:131382200-131385200	Active TSS	Stomach Smooth Muscle	stomach
3	chr6:131382600-131385200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:131382600-131385200	Active TSS	Right Ventricle	heart
5	chr6:131382800-131385200	Active TSS	Aorta	Aorta
6	chr6:131383000-131385200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:131383000-131385200	Active TSS	Psoas Muscle	Psoas
8	chr6:131383000-131385200	Active TSS	Thymus	Thymus
9	chr6:131383000-131385400	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr6:131383200-131385200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:131383400-131385200	Active TSS	Esophagus	oesophagus
12	chr6:131384200-131385200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:131384600-131385200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr6:131384600-131385200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr6:131384600-131385200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr6:131384600-131385200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
17	chr6:131384600-131385200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:131384600-131385200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:131384600-131385200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr6:131384600-131385200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr6:131384600-131385200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:131384600-131385200	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr6:131384600-131385200	Flanking Active TSS	Liver	Liver
24	chr6:131384600-131385200	Flanking Active TSS	Colonic Mucosa	Colon
25	chr6:131384600-131385200	Flanking Active TSS	Fetal Thymus	thymus
26	chr6:131384600-131385200	Flanking Active TSS	Dnd41	blood
27	chr6:131384600-131385200	Flanking Active TSS	GM12878-XiMat	blood
28	chr6:131384600-131385200	Flanking Active TSS	HMEC	breast
29	chr6:131384600-131385200	Flanking Active TSS	HSMMtube	muscle
30	chr6:131384600-131385200	Flanking Active TSS	NHLF	lung
31	chr6:131384600-131385400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:131384600-131385400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr6:131384600-131385400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:131384600-131385400	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr6:131384600-131385400	Flanking Active TSS	HepG2	liver
36	chr6:131384800-131385200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:131384800-131385200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:131384800-131385200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
39	chr6:131384800-131385200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:131384800-131385200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
41	chr6:131384800-131385200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
42	chr6:131384800-131385200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:131384800-131385200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:131384800-131385200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:131384800-131385200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr6:131384800-131385200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr6:131384800-131385200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:131384800-131385200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:131384800-131385200	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr6:131384800-131385200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links