Variant report

Variant	rs7308021
Chromosome Location	chr12:62859420-62859421
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	CEBPB	chr12:62859269-62859588	A549	lung:	n/a	chr12:62859390-62859401 chr12:62859391-62859402 chr12:62859327-62859338
2	CEBPB	chr12:62859243-62859737	Hela-S3	cervix:	n/a	chr12:62859390-62859401 chr12:62859391-62859402 chr12:62859327-62859338
3	MXI1	chr12:62859406-62861970	SK-N-SH	brain:	n/a	n/a
4	CEBPB	chr12:62859254-62859585	IMR90	lung:	n/a	chr12:62859390-62859401 chr12:62859391-62859402 chr12:62859327-62859338
5	CEBPB	chr12:62859252-62859580	HepG2	liver:	n/a	chr12:62859390-62859401 chr12:62859391-62859402 chr12:62859327-62859338
6	CEBPB	chr12:62859242-62859645	K562	blood:	n/a	chr12:62859390-62859401 chr12:62859391-62859402 chr12:62859327-62859338

No.	Distal block	Cell Line	Cell type
1	chr12:62859264..62862504-chr12:62994446..62997723,4	K562	blood:
2	chr12:62858052..62860606-chr12:62997012..62999153,2	K562	blood:
3	chr12:62859326..62863326-chr12:62876630..62881311,5	K562	blood:
4	chr12:62859286..62861275-chr12:62995759..62997449,2	MCF-7	breast:

Variant related genes	Relation type
MON2	TF binding region
ENSG00000199179	Chromatin interaction
ENSG00000257568	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000221949	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10128830	0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10128959	0.80[ASN][1000 genomes]
rs10161549	0.83[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs10219555	0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs10219765	0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10735907	0.92[ASN][1000 genomes]
rs10735909	0.90[ASN][1000 genomes]
rs10747963	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747965	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747966	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10784299	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10784302	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10784303	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10784306	0.81[ASN][1000 genomes]
rs10784307	0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10877851	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877860	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10877863	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10877865	0.93[ASN][1000 genomes]
rs10877866	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10877868	0.89[ASN][1000 genomes]
rs10877869	0.86[ASN][1000 genomes]
rs10877872	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877873	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs10877876	0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10877880	0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs10877885	0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs10877886	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs10877888	0.81[CHB][hapmap]
rs11174493	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11174497	0.94[ASN][1000 genomes]
rs11174507	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11174513	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11174520	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs11174534	0.89[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs11174538	0.85[JPT][hapmap]
rs11174540	0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11174541	0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11174542	0.84[ASN][1000 genomes]
rs11174550	0.80[ASN][1000 genomes]
rs11495588	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12227568	0.84[ASN][1000 genomes]
rs12300696	0.85[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12305077	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12309683	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12357	0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs12371971	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12371972	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12578200	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12581171	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12809279	0.91[ASN][1000 genomes]
rs12810119	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1498713	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2047478	0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2047479	0.84[ASN][1000 genomes]
rs2141777	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2220980	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4763021	0.83[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4763174	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs4763177	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs6581452	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6581454	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7134302	0.88[ASN][1000 genomes]
rs7136993	0.80[ASN][1000 genomes]
rs7294404	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7298782	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7302027	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.93[ASN][1000 genomes]
rs7316612	0.88[ASN][1000 genomes]
rs7957417	0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7975183	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7975560	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][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	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7308021	C12orf61	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62853600-62860000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:62859200-62859600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr12:62859400-62859600	Enhancers	Primary T cells from cord blood	blood
4	chr12:62859400-62859600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:62859400-62859600	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr12:62859400-62859600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr12:62859400-62859600	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr12:62859400-62859600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr12:62859400-62859600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr12:62859400-62859600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr12:62859400-62859600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:62859400-62859600	Active TSS	Liver	Liver
13	chr12:62859400-62859600	Active TSS	Brain Hippocampus Middle	brain
14	chr12:62859400-62859600	Enhancers	Brain Substantia Nigra	brain
15	chr12:62859400-62859600	Enhancers	Colon Smooth Muscle	Colon
16	chr12:62859400-62859600	Enhancers	Fetal Brain Female	brain
17	chr12:62859400-62859600	Enhancers	Fetal Intestine Small	intestine
18	chr12:62859400-62859600	Enhancers	Rectal Smooth Muscle	rectum
19	chr12:62859400-62859600	Enhancers	Stomach Mucosa	stomach
20	chr12:62859400-62859600	Active TSS	Stomach Smooth Muscle	stomach
21	chr12:62859400-62859600	Enhancers	GM12878-XiMat	blood
22	chr12:62859400-62859600	Active TSS	Hela-S3	cervix
23	chr12:62859400-62859600	Enhancers	HepG2	liver
24	chr12:62859400-62859600	Enhancers	HMEC	breast
25	chr12:62859400-62859600	Enhancers	K562	blood
26	chr12:62859400-62859600	Enhancers	NHEK	skin
27	chr12:62859400-62859800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr12:62859400-62859800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:62859400-62859800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr12:62859400-62860200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:62859400-62860200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:62859400-62860200	Flanking Active TSS	Dnd41	blood
33	chr12:62859400-62861800	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr12:62859400-62862600	Active TSS	Duodenum Mucosa	Duodenum
35	chr12:62859400-62863600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links