Variant report

Variant	rs2239200
Chromosome Location	chr12:120538651-120538652
allele	C/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	MYC	chr12:120538525-120538691	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr12:120538614-120538747	HUVEC	blood vessel:	n/a	n/a
3	MAX	chr12:120538450-120538805	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr12:120538290-120538714	GM12878	blood:	n/a	n/a
5	CTCF	chr12:120538620-120538770	SK-N-SH_RA	brain:	n/a	chr12:120538714-120538732
6	NFIC	chr12:120538297-120538949	SK-N-SH	brain:	n/a	chr12:120538578-120538595 chr12:120538578-120538594
7	MXI1	chr12:120538037-120538952	IMR90	lung:	n/a	n/a
8	POLR2A	chr12:120538516-120538753	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:120537387-120538675	GM12878	blood:	n/a	n/a
10	MXI1	chr12:120538132-120539565	SK-N-SH	brain:	n/a	chr12:120539535-120539544

No.	Distal block	Cell Line	Cell type
1	chr12:120537048..120541245-chr12:120553607..120557723,6	MCF-7	breast:
2	chr12:120426493..120428297-chr12:120534910..120538709,3	MCF-7	breast:
3	chr12:120537177..120551260-chr12:120551865..120557471,32	MCF-7	breast:
4	chr12:120538101..120541195-chr12:120726908..120731130,5	MCF-7	breast:
5	chr12:120534104..120540073-chr12:120552292..120555790,7	K562	blood:
6	chr12:120515805..120518721-chr12:120536191..120539691,3	MCF-7	breast:

Variant related genes	Relation type
RAB35	TF binding region
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000135127	Chromatin interaction
ENSG00000111737	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10128766	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap];0.86[ASN][1000 genomes]
rs10400498	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10400560	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849731	0.86[ASN][1000 genomes]
rs10849732	0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10849735	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10849736	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.92[ASN][1000 genomes]
rs11064987	0.84[ASN][1000 genomes]
rs11064988	0.85[ASN][1000 genomes]
rs11064996	0.87[ASN][1000 genomes]
rs11065003	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs11833221	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12310269	0.87[ASN][1000 genomes]
rs12310591	0.92[ASN][1000 genomes]
rs12313413	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12318774	0.86[ASN][1000 genomes]
rs12320793	0.84[ASN][1000 genomes]
rs12322236	0.86[ASN][1000 genomes]
rs12422923	0.92[ASN][1000 genomes]
rs16949901	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16949946	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16949961	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17841967	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239201	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][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]
rs2239202	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239204	0.99[ASN][1000 genomes]
rs2240311	0.87[CHB][hapmap]
rs2283359	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283360	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283361	0.82[ASN][1000 genomes]
rs2286040	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28726166	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3852586	0.83[CHB][hapmap]
rs4767869	0.86[ASN][1000 genomes]
rs4767871	0.92[ASN][1000 genomes]
rs4767872	0.92[ASN][1000 genomes]
rs4767875	0.92[ASN][1000 genomes]
rs4767876	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58272825	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59168361	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60466490	0.92[ASN][1000 genomes]
rs6490281	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs6490284	0.83[CHB][hapmap]
rs7298183	0.86[ASN][1000 genomes]
rs7298727	0.86[ASN][1000 genomes]
rs7300023	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]
rs7306739	0.83[CHB][hapmap]
rs7312971	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7397339	0.92[ASN][1000 genomes]
rs7958402	0.86[ASN][1000 genomes]
rs7958497	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs7965829	0.86[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7968557	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7978927	0.91[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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120525600-120539200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:120525600-120551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:120525800-120539200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:120525800-120553400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:120527400-120546800	Strong transcription	Thymus	Thymus
6	chr12:120527600-120538800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:120527600-120539200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:120527600-120539800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:120527600-120540400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:120527600-120546000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:120528600-120538800	Strong transcription	NHEK	skin
12	chr12:120529000-120540400	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:120529000-120546800	Strong transcription	Dnd41	blood
14	chr12:120529600-120543000	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:120529800-120539200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:120529800-120542200	Strong transcription	Fetal Intestine Large	intestine
17	chr12:120530000-120539200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:120530800-120540400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr12:120532200-120539000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:120532200-120539600	Strong transcription	Primary T cells from cord blood	blood
21	chr12:120532400-120539000	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr12:120532400-120539800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:120532600-120539000	Strong transcription	GM12878-XiMat	blood
24	chr12:120532600-120539200	Strong transcription	Fetal Intestine Small	intestine
25	chr12:120532600-120539400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:120532600-120539400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:120532600-120539600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:120532800-120541600	Weak transcription	K562	blood
29	chr12:120533600-120542800	Strong transcription	A549	lung
30	chr12:120533800-120538800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:120533800-120553000	Weak transcription	Fetal Kidney	kidney
32	chr12:120534000-120539200	Strong transcription	Liver	Liver
33	chr12:120534200-120539200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:120534200-120542800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:120534200-120542800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:120534200-120542800	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:120534400-120553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:120534600-120546800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:120534600-120547200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:120534600-120548200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:120534800-120539600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:120536000-120541800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:120536200-120543000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:120536400-120538800	Weak transcription	HSMMtube	muscle
45	chr12:120536600-120538800	Weak transcription	Stomach Mucosa	stomach
46	chr12:120536600-120538800	Weak transcription	NH-A	brain
47	chr12:120536600-120539000	Strong transcription	Primary B cells from cord blood	blood
48	chr12:120536800-120540800	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:120536800-120541200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:120536800-120541800	Genic enhancers	Esophagus	oesophagus

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