Variant report

Variant	rs12112423
Chromosome Location	chr7:11580284-11580285
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1023525	1.00[JPT][hapmap]
rs10240343	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10240511	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10242744	0.81[CHD][hapmap]
rs1034739	0.81[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap]
rs10428944	0.93[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10486153	0.80[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs10486155	0.93[CEU][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12112567	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[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]
rs12113763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12699205	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12699206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12699208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12699211	0.81[CHD][hapmap];0.80[MEX][hapmap]
rs12699223	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12699224	0.93[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12699225	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12699233	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12699236	0.85[AMR][1000 genomes]
rs12699243	0.81[AMR][1000 genomes]
rs12699244	0.81[AMR][1000 genomes]
rs12699246	0.81[GIH][hapmap];0.93[MEX][hapmap]
rs13228651	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13229007	0.80[CEU][hapmap]
rs13238469	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17164736	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs17164737	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs17164738	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs17164739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs17164805	0.86[ASW][hapmap];0.93[CEU][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17634217	1.00[JPT][hapmap]
rs2040816	0.80[CEU][hapmap];0.83[AMR][1000 genomes]
rs2040817	0.86[CEU][hapmap];0.88[AMR][1000 genomes]
rs2072139	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074607	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2107144	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2158260	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2214590	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2214591	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2354953	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2883564	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35833899	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4291151	0.93[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4443556	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4443557	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4504531	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4571634	0.93[CEU][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57445589	0.84[ASN][1000 genomes]
rs59758867	0.84[ASN][1000 genomes]
rs59956574	0.84[ASN][1000 genomes]
rs60572471	0.84[ASN][1000 genomes]
rs60743469	0.90[ASN][1000 genomes]
rs67541992	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6942629	0.87[CEU][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6946249	0.90[ASN][1000 genomes]
rs6946819	0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6958901	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6964073	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6968824	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6972615	1.00[JPT][hapmap]
rs6975510	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6980164	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs6980325	0.82[CEU][hapmap]
rs73286870	0.84[ASN][1000 genomes]
rs73286874	0.84[ASN][1000 genomes]
rs73286880	0.84[ASN][1000 genomes]
rs73286882	0.88[ASN][1000 genomes]
rs73286889	0.84[ASN][1000 genomes]
rs73286890	0.84[ASN][1000 genomes]
rs73286893	0.83[ASN][1000 genomes]
rs73288805	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs739754	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs739755	0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs739756	0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs739758	0.89[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs757217	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs757218	0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs764195	0.80[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap]
rs7788442	0.83[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs7790988	0.86[AMR][1000 genomes]
rs7792687	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7792827	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7804875	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7805116	0.89[ASW][hapmap];0.82[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes]
rs7811211	0.93[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028326	chr7:11221209-11754436	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv538733	chr7:11221209-11754436	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830903	chr7:11384957-11586376	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1023665	chr7:11457493-11773517	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv887606	chr7:11473561-11771288	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1028614	chr7:11511684-11596934	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv464366	chr7:11522525-11602899	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv606200	chr7:11522525-11602899	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv887609	chr7:11547284-11581121	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv887610	chr7:11548082-11581121	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:11564800-11582200	Weak transcription	A549	lung
2	chr7:11565000-11582200	Weak transcription	Fetal Kidney	kidney
3	chr7:11570400-11592000	Weak transcription	Fetal Brain Male	brain
4	chr7:11575600-11582000	Weak transcription	Fetal Brain Female	brain
5	chr7:11577400-11581000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:11577400-11615200	Weak transcription	Placenta	Placenta
7	chr7:11577800-11580600	Enhancers	Fetal Lung	lung
8	chr7:11578000-11581200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:11578200-11581400	Enhancers	Primary hematopoietic stem cells	blood
10	chr7:11578400-11581600	Enhancers	Dnd41	blood
11	chr7:11579200-11580600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:11579200-11580800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:11579400-11580400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:11579400-11580400	Enhancers	Hela-S3	cervix
15	chr7:11579400-11580600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:11579400-11580600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr7:11579400-11580600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr7:11579400-11580600	Enhancers	HMEC	breast
19	chr7:11579800-11580400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr7:11579800-11580600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:11579800-11580600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr7:11579800-11580600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:11579800-11580600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:11579800-11580600	Enhancers	Fetal Thymus	thymus
25	chr7:11579800-11580600	Enhancers	HSMM	muscle
26	chr7:11579800-11580600	Enhancers	NHEK	skin
27	chr7:11579800-11580800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr7:11579800-11581200	Enhancers	NH-A	brain
29	chr7:11580000-11580400	Enhancers	Colon Smooth Muscle	Colon
30	chr7:11580000-11580400	Enhancers	Placenta Amnion	Placenta Amnion
31	chr7:11580000-11580400	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr7:11580000-11580600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:11580000-11580600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:11580000-11580600	Enhancers	Fetal Muscle Leg	muscle
35	chr7:11580000-11580600	Enhancers	NHDF-Ad	bronchial
36	chr7:11580200-11580600	Enhancers	HUVEC	blood vessel
37	chr7:11580200-11581000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:11580200-11581200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr7:11580200-11581200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:11580200-11582600	Weak transcription	Liver	Liver
41	chr7:11580200-11583000	Weak transcription	Adipose Nuclei	Adipose

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