Variant report

Variant	rs7300023
Chromosome Location	chr12:120542487-120542488
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120542078..120544361-chr12:120724685..120726215,2	MCF-7	breast:
2	chr12:120541504..120543197-chr12:120554093..120555992,2	K562	blood:
3	chr12:120539799..120542911-chr12:120545962..120548810,4	MCF-7	breast:
4	chr12:120537177..120551260-chr12:120551865..120557471,32	MCF-7	breast:
5	chr12:120539029..120543839-chr12:120726926..120732179,7	MCF-7	breast:
6	chr12:120541333..120544024-chr12:120545087..120548824,4	K562	blood:

Variant related genes	Relation type
ENSG00000111737	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10128766	0.86[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs10400498	0.86[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10400560	0.91[ASN][1000 genomes]
rs10849731	0.85[ASN][1000 genomes]
rs10849732	0.91[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10849735	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10849736	0.86[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.91[ASN][1000 genomes]
rs11064987	0.84[ASN][1000 genomes]
rs11064988	0.84[ASN][1000 genomes]
rs11064996	0.86[ASN][1000 genomes]
rs11065003	0.86[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs11833221	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12310269	0.86[ASN][1000 genomes]
rs12310591	0.91[ASN][1000 genomes]
rs12313413	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12318774	0.85[ASN][1000 genomes]
rs12320793	0.84[ASN][1000 genomes]
rs12322236	0.85[ASN][1000 genomes]
rs12422923	0.91[ASN][1000 genomes]
rs16949901	0.91[ASN][1000 genomes]
rs16949946	0.86[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16949961	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17841967	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239200	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239201	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239202	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2239203	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239204	0.99[ASN][1000 genomes]
rs2240311	0.86[CHB][hapmap]
rs2283359	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2283360	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2283361	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2286040	0.86[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28726166	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3852586	0.82[CHB][hapmap]
rs4767869	0.85[ASN][1000 genomes]
rs4767871	0.91[ASN][1000 genomes]
rs4767872	0.91[ASN][1000 genomes]
rs4767875	0.91[ASN][1000 genomes]
rs4767876	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58272825	0.91[ASN][1000 genomes]
rs59168361	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60466490	0.91[ASN][1000 genomes]
rs6490281	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs6490284	0.83[CHB][hapmap]
rs7298183	0.85[ASN][1000 genomes]
rs7298727	0.85[ASN][1000 genomes]
rs7306739	0.83[CHB][hapmap]
rs7312971	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7397339	0.91[ASN][1000 genomes]
rs7958402	0.85[ASN][1000 genomes]
rs7958497	0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.83[ASN][1000 genomes]
rs7965829	0.86[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7968557	0.86[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7978927	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv560434	chr12:120534147-120545718	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7300023	CCDC64	cis	cerebellum	SCAN
rs7300023	VPS33A	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120525600-120551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:120525800-120553400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:120527400-120546800	Strong transcription	Thymus	Thymus
4	chr12:120527600-120546000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:120529000-120546800	Strong transcription	Dnd41	blood
6	chr12:120529600-120543000	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:120533600-120542800	Strong transcription	A549	lung
8	chr12:120533800-120553000	Weak transcription	Fetal Kidney	kidney
9	chr12:120534200-120542800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:120534200-120542800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:120534200-120542800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:120534400-120553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:120534600-120546800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:120534600-120547200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:120534600-120548200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:120536200-120543000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:120537000-120543800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:120537400-120542600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr12:120537800-120543400	Genic enhancers	Spleen	Spleen
20	chr12:120537800-120544400	Genic enhancers	Placenta	Placenta
21	chr12:120538200-120543000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:120539200-120552600	Weak transcription	Fetal Brain Male	brain
23	chr12:120539600-120542800	Weak transcription	Primary B cells from cord blood	blood
24	chr12:120539600-120545800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr12:120539600-120546600	Strong transcription	Fetal Brain Female	brain
26	chr12:120539600-120551600	Weak transcription	Fetal Lung	lung
27	chr12:120539600-120552200	Strong transcription	Fetal Stomach	stomach
28	chr12:120539800-120544200	Strong transcription	Liver	Liver
29	chr12:120540000-120543200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:120540000-120546400	Weak transcription	Colon Smooth Muscle	Colon
31	chr12:120540000-120546800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:120540000-120547600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr12:120540000-120553000	Weak transcription	HSMMtube	muscle
34	chr12:120540200-120542800	Weak transcription	Stomach Mucosa	stomach
35	chr12:120540200-120543400	Strong transcription	Pancreas	Pancrea
36	chr12:120540200-120544000	Strong transcription	HUVEC	blood vessel
37	chr12:120540200-120545400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:120540400-120543000	Weak transcription	Fetal Heart	heart
39	chr12:120540400-120543200	Strong transcription	Colonic Mucosa	Colon
40	chr12:120540400-120544000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:120540400-120544600	Strong transcription	Brain Germinal Matrix	brain
42	chr12:120540400-120546000	Strong transcription	Primary T cells from cord blood	blood
43	chr12:120540400-120546600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:120540400-120546600	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr12:120540600-120542600	Strong transcription	Brain Cingulate Gyrus	brain
46	chr12:120540600-120542800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:120540600-120543400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:120540600-120544000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr12:120540600-120544200	Strong transcription	HepG2	liver
50	chr12:120540600-120544400	Strong transcription	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