Variant report

Variant	rs7342365
Chromosome Location	chr12:49861912-49861913
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49848778..49850506-chr12:49860087..49862651,2	MCF-7	breast:
2	chr12:49759346..49761819-chr12:49860878..49862664,2	K562	blood:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10160947	0.83[ASN][1000 genomes]
rs10161131	0.83[ASN][1000 genomes]
rs10506284	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10506285	1.00[JPT][hapmap]
rs10875948	1.00[CHB][hapmap]
rs11168967	1.00[CHB][hapmap]
rs11168981	1.00[JPT][hapmap]
rs11168988	1.00[ASN][1000 genomes]
rs11169015	1.00[ASN][1000 genomes]
rs11169016	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11169017	1.00[ASN][1000 genomes]
rs11169027	1.00[ASN][1000 genomes]
rs11169048	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs11169058	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11169059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11611743	1.00[ASN][1000 genomes]
rs11834161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11835037	1.00[CHB][hapmap]
rs11837234	1.00[CHB][hapmap]
rs12296440	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12299282	1.00[ASN][1000 genomes]
rs12301632	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12302036	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12305716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12306118	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12306212	1.00[ASN][1000 genomes]
rs12306645	1.00[ASN][1000 genomes]
rs12306866	1.00[JPT][hapmap]
rs12309053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12310129	1.00[JPT][hapmap]
rs12310836	0.84[AMR][1000 genomes]
rs12314428	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12315996	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12316170	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12318618	1.00[CHB][hapmap]
rs12318633	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12320284	1.00[ASN][1000 genomes]
rs12322319	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322335	1.00[CHB][hapmap]
rs12322561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12581343	1.00[CHB][hapmap]
rs12581428	1.00[CHB][hapmap]
rs17123696	1.00[JPT][hapmap]
rs17123751	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17123790	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17197593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1874910	1.00[JPT][hapmap]
rs2236746	1.00[CHB][hapmap]
rs2270741	1.00[JPT][hapmap]
rs2272478	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28450055	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847764	1.00[CHB][hapmap]
rs4144469	1.00[JPT][hapmap]
rs57108124	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57601151	1.00[ASN][1000 genomes]
rs59250459	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61340540	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580707	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6580709	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6580710	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580711	1.00[ASN][1000 genomes]
rs6580716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132684	1.00[ASN][1000 genomes]
rs7139061	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7294648	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7294973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7295162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295247	1.00[CHB][hapmap]
rs7309997	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73295291	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73295300	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297209	1.00[ASN][1000 genomes]
rs73297210	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297243	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73301240	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7342318	1.00[CHB][hapmap]
rs7342384	1.00[CHB][hapmap]
rs74089066	1.00[ASN][1000 genomes]
rs7955541	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7961032	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7962951	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7964718	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7969010	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs7969099	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7976165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9919740	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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

No data

Chromatin state (count:66 , 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	chr12:49823400-49876000	Weak transcription	Osteobl	bone
3	chr12:49828000-49863400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:49839200-49876000	Weak transcription	Fetal Thymus	thymus
5	chr12:49840200-49900600	Weak transcription	Pancreas	Pancrea
6	chr12:49840600-49875800	Weak transcription	Hela-S3	cervix
7	chr12:49846000-49879800	Weak transcription	Fetal Lung	lung
8	chr12:49846400-49878400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr12:49849400-49875800	Weak transcription	HepG2	liver
10	chr12:49849600-49869800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:49850400-49876000	Weak transcription	Fetal Intestine Large	intestine
12	chr12:49850400-49876000	Weak transcription	Small Intestine	intestine
13	chr12:49850400-49878800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:49850400-49911000	Weak transcription	K562	blood
15	chr12:49850600-49876200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:49853200-49876000	Weak transcription	HSMMtube	muscle
17	chr12:49853200-49913400	Weak transcription	Thymus	Thymus
18	chr12:49854400-49878400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:49855200-49872600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:49855400-49869800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:49855600-49870000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:49856400-49869800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:49856400-49870200	Weak transcription	Gastric	stomach
24	chr12:49856400-49872600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:49856400-49883400	Weak transcription	Brain Anterior Caudate	brain
26	chr12:49856600-49869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:49856600-49872800	Weak transcription	Fetal Muscle Leg	muscle
28	chr12:49856600-49874400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:49856600-49875800	Weak transcription	Adipose Nuclei	Adipose
30	chr12:49856600-49890200	Weak transcription	Primary T cells from cord blood	blood
31	chr12:49856600-49890200	Weak transcription	Ovary	ovary
32	chr12:49856800-49862400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:49856800-49862400	Weak transcription	Fetal Intestine Small	intestine
34	chr12:49856800-49864000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr12:49856800-49864400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:49856800-49864400	Weak transcription	Right Atrium	heart
37	chr12:49856800-49865000	Weak transcription	GM12878-XiMat	blood
38	chr12:49856800-49866800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:49856800-49867400	Weak transcription	HUVEC	blood vessel
40	chr12:49856800-49868600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:49856800-49869200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:49856800-49869600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:49856800-49869800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:49856800-49869800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:49856800-49869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:49856800-49869800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr12:49856800-49869800	Weak transcription	Fetal Stomach	stomach
48	chr12:49856800-49870000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:49856800-49872600	Weak transcription	NHEK	skin
50	chr12:49856800-49876000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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