Variant report

Variant	rs6539695
Chromosome Location	chr12:83233045-83233046
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:83232613..83233339-chr16:75834473..75835318,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10466960	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10506884	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11115457	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11115458	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11115459	0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12300038	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12304267	0.89[ASN][1000 genomes]
rs12317660	0.93[ASN][1000 genomes]
rs17010056	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17010066	0.88[JPT][hapmap]
rs17010069	0.88[CEU][hapmap];0.88[JPT][hapmap]
rs1703105	0.88[JPT][hapmap]
rs1703107	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6539694	0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7137977	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7301204	0.95[ASN][1000 genomes]
rs7304237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7313758	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs73358271	0.86[ASN][1000 genomes]
rs73358284	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73358290	0.81[ASN][1000 genomes]
rs7979960	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9651971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv2758315	chr12:83101045-83357621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2759911	chr12:83101045-83357621	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv2755991	chr12:83105631-83248605	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv2754173	chr12:83125000-83245838	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv2756046	chr12:83166956-83245838	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	esv2755875	chr12:83166956-83248605	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	nsv430520	chr12:83166956-83271602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	esv2752707	chr12:83168113-83245838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
15	esv2753376	chr12:83168113-83245838	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
16	esv2754178	chr12:83168113-83245838	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	nsv437765	chr12:83230454-83271933	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83196400-83250800	Weak transcription	Fetal Muscle Leg	muscle
2	chr12:83206600-83250000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:83206600-83255200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:83212400-83257000	Weak transcription	Gastric	stomach
5	chr12:83214200-83250800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:83216800-83240000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:83226600-83234600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:83228000-83241600	Weak transcription	Fetal Kidney	kidney
9	chr12:83229000-83233600	Weak transcription	Fetal Stomach	stomach
10	chr12:83229000-83233800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:83229200-83236800	Enhancers	Brain Hippocampus Middle	brain
12	chr12:83229600-83235200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:83229600-83252000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:83229800-83233800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:83230000-83236800	Enhancers	Brain Cingulate Gyrus	brain
16	chr12:83230200-83233800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:83230800-83236400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:83231800-83233200	Enhancers	Fetal Heart	heart
19	chr12:83231800-83234200	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr12:83232200-83234800	Enhancers	Brain Substantia Nigra	brain
21	chr12:83232400-83235200	Weak transcription	Fetal Brain Male	brain
22	chr12:83232400-83236800	Enhancers	Brain Angular Gyrus	brain
23	chr12:83232400-83242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:83232600-83233200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr12:83232800-83234400	Enhancers	Brain Anterior Caudate	brain
26	chr12:83232800-83243400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:83233000-83233800	Weak transcription	Fetal Lung	lung
28	chr12:83233000-83234000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:83233000-83234400	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:83233000-83235600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:83233000-83242400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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