Variant report

Variant	rs12322561
Chromosome Location	chr12:49909157-49909158
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49739423..49741666-chr12:49907974..49910735,2	MCF-7	breast:
2	chr12:49758876..49762155-chr12:49906533..49909731,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178401	Chromatin interaction
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10506284	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10506285	1.00[JPT][hapmap]
rs11168981	1.00[JPT][hapmap]
rs11169016	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11169048	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11169049	1.00[ASN][1000 genomes]
rs11169058	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11169059	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11169080	0.88[GIH][hapmap]
rs11830144	1.00[CHD][hapmap]
rs11834161	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap]
rs12296440	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12300817	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301632	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12305716	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306118	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12306866	1.00[JPT][hapmap]
rs12309053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310129	1.00[JPT][hapmap]
rs12314428	1.00[ASN][1000 genomes]
rs12315996	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12316170	1.00[ASN][1000 genomes]
rs12318618	1.00[CHB][hapmap]
rs12318633	1.00[ASN][1000 genomes]
rs12322571	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581343	1.00[CHB][hapmap]
rs12581428	1.00[CHB][hapmap]
rs1317131	1.00[CHD][hapmap]
rs17123696	1.00[JPT][hapmap]
rs17123751	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17123764	1.00[CHD][hapmap]
rs17123790	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17123865	1.00[CHB][hapmap]
rs17197593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1874910	1.00[JPT][hapmap]
rs2270741	1.00[JPT][hapmap]
rs2272478	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3887727	0.88[GIH][hapmap]
rs4144469	1.00[JPT][hapmap]
rs4569075	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4641552	1.00[CHD][hapmap]
rs57200170	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57882760	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60808917	1.00[ASN][1000 genomes]
rs6580707	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6580709	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6580716	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs7139061	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7294648	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7294973	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs7295162	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs7309997	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73301240	1.00[ASN][1000 genomes]
rs73301259	1.00[ASN][1000 genomes]
rs7342365	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7955541	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7962951	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7969099	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7976165	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs9919739	0.83[ASN][1000 genomes]
rs9919740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9919807	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv518746	chr12:49870964-49924637	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49823000-49915800	Weak transcription	Primary B cells from cord blood	blood
2	chr12:49850400-49911000	Weak transcription	K562	blood
3	chr12:49853200-49913400	Weak transcription	Thymus	Thymus
4	chr12:49869600-49918400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:49873000-49918800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:49873200-49918600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:49874800-49914200	Weak transcription	Fetal Kidney	kidney
8	chr12:49876400-49911200	Weak transcription	Adipose Nuclei	Adipose
9	chr12:49876800-49916200	Weak transcription	Psoas Muscle	Psoas
10	chr12:49878600-49918600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr12:49880400-49916000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:49882200-49918800	Weak transcription	Colonic Mucosa	Colon
13	chr12:49882400-49918400	Weak transcription	Lung	lung
14	chr12:49882600-49916400	Weak transcription	Aorta	Aorta
15	chr12:49884200-49918400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:49884200-49918600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:49884600-49916400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:49886000-49918400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:49886400-49918200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:49888800-49927800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:49890800-49918600	Weak transcription	Brain Anterior Caudate	brain
22	chr12:49890800-49918600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:49891000-49916600	Weak transcription	Ovary	ovary
24	chr12:49893600-49915200	Weak transcription	Placenta	Placenta
25	chr12:49894000-49916600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr12:49894000-49919600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:49894400-49915000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:49894400-49915400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:49895400-49914600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr12:49896000-49916800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:49896200-49911000	Weak transcription	Primary T cells from cord blood	blood
32	chr12:49896200-49911200	Weak transcription	Fetal Intestine Large	intestine
33	chr12:49896400-49914600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:49896400-49915000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:49896400-49916600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:49896600-49913400	Weak transcription	Fetal Stomach	stomach
37	chr12:49896800-49916400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:49896800-49916400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:49896800-49916600	Weak transcription	Fetal Thymus	thymus
40	chr12:49898200-49916400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr12:49898200-49918400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr12:49900000-49916400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:49900400-49914800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr12:49900400-49915000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:49900600-49911200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:49900600-49916400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:49900600-49916600	Weak transcription	Left Ventricle	heart
48	chr12:49901200-49910800	Weak transcription	GM12878-XiMat	blood
49	chr12:49901200-49912600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:49904400-49913400	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links