Variant report

Variant	rs6490267
Chromosome Location	chr12:120106376-120106377
allele	G/T
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	chr12:120105556-120106452	K562	blood:	n/a	n/a
2	BCLAF1	chr12:120105253-120106535	GM12878	blood:	n/a	chr12:120105664-120105673 chr12:120105754-120105763
3	POLR2A	chr12:120105453-120106408	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:120105507-120106792	GM12891	blood:	n/a	n/a
5	POLR2A	chr12:120105270-120107198	GM12878	blood:	n/a	n/a
6	MXI1	chr12:120104725-120106494	GM12878	blood:	n/a	n/a
7	ZNF384	chr12:120105499-120106574	K562	blood:	n/a	n/a
8	STAT5A	chr12:120105365-120106593	GM12878	blood:	n/a	n/a
9	GABPA	chr12:120105231-120106442	HL-60	blood:	n/a	chr12:120105759-120105766 chr12:120105598-120105612 chr12:120105669-120105676
10	POLR2A	chr12:120105542-120106494	HepG2	liver:	n/a	n/a
11	GABPA	chr12:120105250-120106627	MCF-7	breast:	n/a	chr12:120105759-120105766 chr12:120105598-120105612 chr12:120105669-120105676
12	POLR2A	chr12:120105624-120107081	K562	blood:	n/a	n/a
13	POLR2A	chr12:120105522-120106463	GM12891	blood:	n/a	n/a
14	ZNF263	chr12:120105393-120106417	HEK293-T-REx	kidney:	n/a	n/a
15	POLR2A	chr12:120105391-120106433	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:120105357-120106510	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr12:120104759-120106596	GM12891	blood:	n/a	n/a
18	MAZ	chr12:120105325-120106481	K562	blood:	n/a	n/a
19	WRNIP1	chr12:120105248-120106743	GM12878	blood:	n/a	n/a
20	GABPA	chr12:120105180-120106723	A549	lung:	n/a	chr12:120105759-120105766 chr12:120105598-120105612 chr12:120105669-120105676
21	MAZ	chr12:120105302-120106535	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:120105448-120106577	HUVEC	blood vessel:	n/a	n/a
23	PML	chr12:120105292-120106391	K562	blood:	n/a	chr12:120106256-120106264
24	MXI1	chr12:120105048-120106657	IMR90	lung:	n/a	n/a
25	ELF1	chr12:120105249-120106414	HCT-116	colon:	n/a	chr12:120105754-120105763 chr12:120105759-120105768
26	RCOR1	chr12:120105124-120106522	IMR90	lung:	n/a	n/a
27	POLR2A	chr12:120105482-120106397	MCF-7	breast:	n/a	n/a
28	CCNT2	chr12:120105357-120106879	K562	blood:	n/a	n/a
29	POLR2A	chr12:120105605-120106417	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr12:120105217-120107065	GM12892	blood:	n/a	n/a
31	UBTF	chr12:120105397-120106619	K562	blood:	n/a	n/a
32	POLR2A	chr12:120105402-120106904	GM12892	blood:	n/a	n/a
33	POLR2A	chr12:120105410-120106652	PBDE	blood:	n/a	n/a
34	MAZ	chr12:120105021-120106527	IMR90	lung:	n/a	n/a
35	HEY1	chr12:120105529-120106532	K562	blood:	n/a	n/a
36	MTA3	chr12:120104564-120106691	GM12878	blood:	n/a	n/a
37	GABPA	chr12:120105352-120106384	SK-N-SH	brain:	n/a	chr12:120105759-120105766 chr12:120105598-120105612 chr12:120105669-120105676
38	POLR2A	chr12:120105213-120106803	GM12892	blood:	n/a	n/a
39	POLR2A	chr12:120105570-120106604	K562	blood:	n/a	n/a
40	POLR2A	chr12:120105452-120106580	K562	blood:	n/a	n/a
41	PML	chr12:120104352-120106743	GM12878	blood:	n/a	chr12:120106256-120106264
42	HCFC1	chr12:120104714-120106446	Hela-S3	cervix:	n/a	n/a
43	MTA3	chr12:120105643-120106569	GM12878	blood:	n/a	n/a
44	SIN3AK20	chr12:120105184-120106473	MCF-7	breast:	n/a	n/a
45	CTCF	chr12:120104578-120106752	A549	lung:	n/a	chr12:120105536-120105549 chr12:120105534-120105552 chr12:120105535-120105551
46	POLR2A	chr12:120105425-120106450	K562	blood:	n/a	n/a
47	POLR2A	chr12:120105354-120106459	GM12878	blood:	n/a	n/a
48	POLR2A	chr12:120105572-120106514	GM12891	blood:	n/a	n/a
49	POLR2A	chr12:120105509-120106457	GM12892	blood:	n/a	n/a
50	POLR2A	chr12:120105275-120106828	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120104659..120106467-chr4:174254824..174256542,2	MCF-7	breast:
2	chr12:120104750..120107660-chr12:120111377..120114502,3	MCF-7	breast:
3	chr12:120104335..120107623-chr12:120110345..120114528,7	MCF-7	breast:
4	chr12:118812486..118814761-chr12:120105257..120106996,2	K562	blood:
5	chr12:120105122..120114412-chr12:120115205..120125435,13	MCF-7	breast:
6	chr12:120104565..120106668-chr12:120729361..120730960,2	K562	blood:
7	chr12:120105026..120107337-chr12:120115955..120117891,2	MCF-7	breast:
8	chr12:120105686..120108054-chr12:120134136..120136155,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248636	TF binding region
PRKAB1	TF binding region
ENSG00000122966	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000111725	Chromatin interaction
ENSG00000111707	Chromatin interaction
ENSG00000270482	Chromatin interaction
ENSG00000164104	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10849688	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849690	1.00[ASN][1000 genomes]
rs11064873	0.93[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs175878	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978107	0.93[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978108	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs202983	0.87[MEX][hapmap]
rs278102	0.87[MEX][hapmap]
rs278123	0.92[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278126	0.87[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs278143	0.92[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278144	0.91[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278145	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278147	0.92[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278148	0.92[CEU][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278149	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278151	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278152	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278154	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278155	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930004	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4213	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490266	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304996	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310266	0.93[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960723	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963248	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967558	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972600	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979627	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804667	1.00[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	nsv1052595	chr12:119992580-120132038	Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv541616	chr12:119992580-120132038	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6490267	COQ5	cis	parietal	SCAN
rs6490267	WSB2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120104800-120106400	Active TSS	Fetal Thymus	thymus
2	chr12:120104800-120106800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr12:120104800-120106800	Active TSS	Right Ventricle	heart
4	chr12:120104800-120106800	Active TSS	Stomach Smooth Muscle	stomach
5	chr12:120104800-120107800	Active TSS	Rectal Smooth Muscle	rectum
6	chr12:120105000-120106600	Active TSS	Fetal Muscle Trunk	muscle
7	chr12:120105000-120106600	Active TSS	Right Atrium	heart
8	chr12:120105000-120106800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr12:120105000-120106800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr12:120105000-120106800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:120105000-120106800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr12:120105000-120106800	Active TSS	Brain Anterior Caudate	brain
13	chr12:120105000-120106800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr12:120105000-120106800	Active TSS	HSMMtube	muscle
15	chr12:120105000-120106800	Active TSS	NHDF-Ad	bronchial
16	chr12:120105000-120107000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr12:120105000-120107000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:120105000-120107000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:120105000-120107000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:120105000-120107400	Active TSS	Colonic Mucosa	Colon
21	chr12:120105200-120106400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:120105200-120106400	Active TSS	Brain Angular Gyrus	brain
23	chr12:120105200-120106400	Active TSS	Ovary	ovary
24	chr12:120105200-120106600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:120105200-120106600	Active TSS	Aorta	Aorta
26	chr12:120105200-120106600	Active TSS	Left Ventricle	heart
27	chr12:120105200-120106600	Active TSS	Lung	lung
28	chr12:120105200-120106600	Active TSS	Placenta Amnion	Placenta Amnion
29	chr12:120105200-120106800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:120105200-120106800	Active TSS	H9 Cell Line	embryonic stem cell
31	chr12:120105200-120106800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:120105200-120106800	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr12:120105200-120106800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:120105200-120106800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:120105200-120106800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:120105200-120106800	Active TSS	Brain Substantia Nigra	brain
37	chr12:120105200-120106800	Active TSS	Fetal Kidney	kidney
38	chr12:120105200-120107000	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr12:120105200-120107000	Active TSS	Small Intestine	intestine
40	chr12:120105200-120107400	Active TSS	Fetal Intestine Large	intestine
41	chr12:120105200-120107400	Active TSS	Pancreas	Pancrea
42	chr12:120105200-120107600	Active TSS	Esophagus	oesophagus
43	chr12:120105400-120106400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:120105400-120106400	Active TSS	Primary hematopoietic stem cells	blood
45	chr12:120105400-120106400	Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr12:120105400-120106400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:120105400-120106400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:120105400-120106400	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr12:120105400-120106400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:120105400-120106400	Active TSS	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links