Variant report

Variant	rs2239202
Chromosome Location	chr12:120539307-120539308
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	ELF1	chr12:120538690-120539656	GM12878	blood:	n/a	n/a
2	MTA3	chr12:120538856-120539519	GM12878	blood:	n/a	n/a
3	E2F6	chr12:120539245-120539919	H1-hESC	embryonic stem cell:	n/a	chr12:120539640-120539649
4	STAT5A	chr12:120538916-120539463	GM12878	blood:	n/a	chr12:120539307-120539318
5	RUNX3	chr12:120538983-120539508	GM12878	blood:	n/a	n/a
6	BHLHE40	chr12:120539237-120539484	GM12878	blood:	n/a	n/a
7	RUNX3	chr12:120539015-120539517	GM12878	blood:	n/a	n/a
8	EP300	chr12:120539200-120539364	GM12878	blood:	n/a	chr12:120539309-120539323
9	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	chr12:120537177..120551260-chr12:120551865..120557471,32	MCF-7	breast:
3	chr12:120538101..120541195-chr12:120726908..120731130,5	MCF-7	breast:
4	chr12:120539029..120543839-chr12:120726926..120732179,7	MCF-7	breast:
5	chr12:120534104..120540073-chr12:120552292..120555790,7	K562	blood:
6	chr12:120538883..120540818-chr12:120636912..120639321,2	MCF-7	breast:
7	chr12:120515805..120518721-chr12:120536191..120539691,3	MCF-7	breast:
8	chr12:120524045..120526996-chr12:120539011..120541039,3	MCF-7	breast:

Variant related genes	Relation type
RAB35	TF binding region
ENSG00000135127	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000111737	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10128766	0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10400498	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10400560	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10849731	0.82[ASN][1000 genomes]
rs10849732	0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10849735	0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10849736	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11064987	0.80[ASN][1000 genomes]
rs11064988	0.81[ASN][1000 genomes]
rs11064996	0.83[ASN][1000 genomes]
rs11065003	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11833221	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12310269	0.83[ASN][1000 genomes]
rs12310591	0.88[ASN][1000 genomes]
rs12313413	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12318774	0.82[ASN][1000 genomes]
rs12320793	0.80[ASN][1000 genomes]
rs12322236	0.82[ASN][1000 genomes]
rs12422923	0.88[ASN][1000 genomes]
rs16949901	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16949946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949961	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17841967	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239200	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]
rs2239201	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];0.96[ASN][1000 genomes]
rs2239204	0.95[ASN][1000 genomes]
rs2240311	0.81[CHB][hapmap]
rs2283359	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2283360	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283361	0.81[ASN][1000 genomes]
rs2286040	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28726166	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767869	0.82[ASN][1000 genomes]
rs4767871	0.88[ASN][1000 genomes]
rs4767872	0.88[ASN][1000 genomes]
rs4767875	0.88[ASN][1000 genomes]
rs4767876	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58272825	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59168361	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60466490	0.88[ASN][1000 genomes]
rs6490281	0.81[CHB][hapmap]
rs7298183	0.82[ASN][1000 genomes]
rs7298727	0.82[ASN][1000 genomes]
rs7300023	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]
rs7312971	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7397339	0.88[ASN][1000 genomes]
rs7958402	0.82[ASN][1000 genomes]
rs7958497	0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7965829	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7968557	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7978927	0.87[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	chr12:120525600-120551800	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	chr12:120527600-120539800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:120527600-120540400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:120527600-120546000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:120529000-120540400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:120529000-120546800	Strong transcription	Dnd41	blood
9	chr12:120529600-120543000	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:120529800-120542200	Strong transcription	Fetal Intestine Large	intestine
11	chr12:120530800-120540400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr12:120532200-120539600	Strong transcription	Primary T cells from cord blood	blood
13	chr12:120532400-120539800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:120532600-120539400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:120532600-120539400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:120532600-120539600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:120532800-120541600	Weak transcription	K562	blood
18	chr12:120533600-120542800	Strong transcription	A549	lung
19	chr12:120533800-120553000	Weak transcription	Fetal Kidney	kidney
20	chr12:120534200-120542800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:120534200-120542800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:120534200-120542800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:120534400-120553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:120534600-120546800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:120534600-120547200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:120534600-120548200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:120534800-120539600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:120536000-120541800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr12:120536200-120543000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:120536800-120540800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:120536800-120541200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:120536800-120541800	Genic enhancers	Esophagus	oesophagus
33	chr12:120537000-120539400	Weak transcription	Small Intestine	intestine
34	chr12:120537000-120540800	Genic enhancers	Right Ventricle	heart
35	chr12:120537000-120540800	Weak transcription	Hela-S3	cervix
36	chr12:120537000-120543800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:120537200-120541000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:120537200-120541000	Weak transcription	Osteobl	bone
39	chr12:120537400-120539600	Genic enhancers	Fetal Brain Female	brain
40	chr12:120537400-120541600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:120537400-120541600	Genic enhancers	Gastric	stomach
42	chr12:120537400-120542400	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr12:120537400-120542600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr12:120537600-120540000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:120537600-120540800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:120537600-120541400	Genic enhancers	Fetal Muscle Leg	muscle
47	chr12:120537600-120541600	Genic enhancers	Fetal Muscle Trunk	muscle
48	chr12:120537800-120540200	Weak transcription	Aorta	Aorta
49	chr12:120537800-120540200	Enhancers	Brain Anterior Caudate	brain
50	chr12:120537800-120540200	Genic enhancers	Pancreas	Pancrea

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