Variant report

Variant	rs10774000
Chromosome Location	chr12:1960237-1960238
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	chr12:1959456..1961016-chr12:1962388..1965205,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151062	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10161097	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1076331	0.92[ASN][1000 genomes]
rs11062002	0.99[ASN][1000 genomes]
rs11062003	1.00[ASN][1000 genomes]
rs11062004	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs11062006	1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs11834934	0.88[ASN][1000 genomes]
rs11835900	0.85[ASN][1000 genomes]
rs11836202	0.81[ASN][1000 genomes]
rs12582053	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs16928837	0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs16928848	0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs1860052	0.94[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1860053	0.94[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286368	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2286369	0.88[ASN][1000 genomes]
rs2286371	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286372	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2286374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2286375	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs3815324	0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs4363670	0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs4766425	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4766426	0.92[ASN][1000 genomes]
rs57854489	0.99[ASN][1000 genomes]
rs59620123	1.00[ASN][1000 genomes]
rs59850857	1.00[ASN][1000 genomes]
rs7137553	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7137876	0.92[EUR][1000 genomes]
rs7138458	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs721159	0.87[CHB][hapmap]
rs7303991	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs736310	1.00[ASN][1000 genomes]
rs758162	0.84[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs758163	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758164	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs758166	0.87[CHB][hapmap]
rs917367	0.94[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs917368	1.00[ASN][1000 genomes]
rs960671	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv430442	chr12:1889823-1982151	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv898593	chr12:1901485-1962759	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv898595	chr12:1916838-1962759	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv898596	chr12:1923040-1962759	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv898597	chr12:1928289-1962759	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv934103	chr12:1935388-1984604	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv898598	chr12:1939252-2215448	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1050895	chr12:1941618-1983445	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv898599	chr12:1942752-1989355	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv1038109	chr12:1944485-1985227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	nsv1040260	chr12:1947193-1983782	Weak transcription Bivalent Enhancer Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	nsv556999	chr12:1948947-1981450	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
15	nsv933450	chr12:1949712-1984604	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv1036795	chr12:1950039-1983782	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv1051770	chr12:1950039-1985227	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv1038395	chr12:1950039-1987245	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
19	esv2761720	chr12:1950051-1985239	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv516798	chr12:1952990-1973384	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	nsv430443	chr12:1953866-1982151	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv1045447	chr12:1959333-1993612	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1958200-1962800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:1960000-1960600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:1960000-1961000	Enhancers	Osteobl	bone
4	chr12:1960000-1962000	Enhancers	Fetal Brain Male	brain
5	chr12:1960200-1960800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:1960200-1960800	Enhancers	Muscle Satellite Cultured Cells	--

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