Variant report

Variant	rs12309958
Chromosome Location	chr12:39058608-39058609
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	chr12:39058333..39059128-chr12:39497120..39498000,2	MCF-7	breast:
2	chr12:39058213..39059596-chr12:39300191..39301086,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257718	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1021258	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1038540	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10506128	0.89[MEX][hapmap]
rs10747574	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10875959	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10875962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10875963	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1095577	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11168552	0.86[ASN][1000 genomes]
rs11168979	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169068	0.82[AMR][1000 genomes]
rs11169095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169333	0.81[ASN][1000 genomes]
rs11169407	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12305675	0.89[MEX][hapmap]
rs12318974	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12322362	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12578804	1.00[CEU][hapmap]
rs12580227	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12580606	1.00[CEU][hapmap]
rs12581365	0.82[AMR][1000 genomes]
rs1472657	0.97[ASN][1000 genomes]
rs1486349	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1486350	0.81[ASN][1000 genomes]
rs1486352	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs1486353	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1502631	0.86[ASN][1000 genomes]
rs1615569	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1619885	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs1620594	1.00[CEU][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs1620655	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs1624751	1.00[JPT][hapmap]
rs1684419	1.00[CEU][hapmap];0.81[ASN][1000 genomes]
rs1684420	0.88[JPT][hapmap]
rs1684421	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17126226	1.00[CEU][hapmap]
rs1719846	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap]
rs1827459	0.90[ASN][1000 genomes]
rs1843640	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1843641	1.00[CEU][hapmap]
rs1847181	0.91[ASN][1000 genomes]
rs1872638	0.82[AMR][1000 genomes]
rs1906043	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2101370	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2264357	0.97[ASN][1000 genomes]
rs2388058	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2630779	0.96[ASN][1000 genomes]
rs2653739	0.89[ASN][1000 genomes]
rs2653757	0.97[ASN][1000 genomes]
rs2653762	0.96[ASN][1000 genomes]
rs2653770	0.90[ASN][1000 genomes]
rs2653777	0.86[ASN][1000 genomes]
rs2730891	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2730911	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2730923	0.86[ASN][1000 genomes]
rs2730931	0.85[ASN][1000 genomes]
rs2730938	0.87[ASN][1000 genomes]
rs4238079	0.99[ASN][1000 genomes]
rs4293160	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4767968	0.99[ASN][1000 genomes]
rs5005131	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7297083	1.00[CEU][hapmap]
rs7957523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7976054	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7980889	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs826842	1.00[CEU][hapmap]
rs826878	0.90[JPT][hapmap]
rs826893	0.91[JPT][hapmap]
rs864324	0.91[JPT][hapmap]
rs923200	0.99[ASN][1000 genomes]
rs9645814	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9805091	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422488	chr12:38103874-39070734	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1039821	chr12:38959645-39121578	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1053316	chr12:38959645-39122853	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1043831	chr12:38979065-39117868	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv541479	chr12:38979065-39117868	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1045040	chr12:39038114-39084094	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39045400-39068000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:39046000-39085400	Weak transcription	Aorta	Aorta
3	chr12:39046800-39080400	Weak transcription	Spleen	Spleen
4	chr12:39051600-39080400	Weak transcription	Lung	lung
5	chr12:39051600-39080800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:39054600-39071000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:39055800-39100800	Weak transcription	NHEK	skin
8	chr12:39056000-39061200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:39056000-39080200	Weak transcription	Ovary	ovary
10	chr12:39056000-39092200	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
13	chr12:39056200-39060200	Weak transcription	Liver	Liver
14	chr12:39056200-39078400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:39056200-39078400	Weak transcription	Adipose Nuclei	Adipose
16	chr12:39056200-39079000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:39056200-39080200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:39056800-39083000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:39057400-39070200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:39057400-39083000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:39057600-39060200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:39057600-39072200	Weak transcription	NHDF-Ad	bronchial
23	chr12:39057800-39058800	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr12:39057800-39069000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:39058000-39060000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:39058000-39060800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr12:39058000-39063200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:39058000-39077600	Weak transcription	HMEC	breast
29	chr12:39058200-39079000	Weak transcription	GM12878-XiMat	blood
30	chr12:39058600-39060000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:39058600-39062800	Weak transcription	Primary hematopoietic stem cells	blood

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