Variant report

Variant	rs1860052
Chromosome Location	chr12:1964541-1964542
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr12:1964297-1964791	U2OS	brain:	n/a	n/a
2	ZNF143	chr12:1964512-1964768	H1-hESC	embryonic stem cell:	n/a	n/a
3	USF1	chr12:1964416-1964786	H1-hESC	embryonic stem cell:	n/a	n/a
4	KAP1	chr12:1964381-1964816	HEK293	kidney:	n/a	n/a
5	USF2	chr12:1964502-1964763	H1-hESC	embryonic stem cell:	n/a	n/a
6	USF1	chr12:1964466-1964741	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1956703..1959604-chr12:1963408..1966102,2	MCF-7	breast:

Variant related genes	Relation type
CACNA2D4	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10161058	0.91[ASN][1000 genomes]
rs10161097	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1076331	0.93[ASN][1000 genomes]
rs10774000	0.94[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10848582	0.81[JPT][hapmap]
rs11062002	0.85[ASN][1000 genomes]
rs11062003	0.85[ASN][1000 genomes]
rs11062004	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs11062006	0.84[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs11836202	0.81[ASN][1000 genomes]
rs12582053	0.84[CHB][hapmap]
rs16928837	0.84[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs16928848	0.84[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs1860053	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2286368	0.84[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2286369	0.88[ASN][1000 genomes]
rs2286371	0.85[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2286372	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs2286374	0.93[CEU][hapmap];0.84[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2286375	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs3815324	0.84[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs4363670	0.84[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs4766425	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs4766426	0.93[ASN][1000 genomes]
rs56110511	0.81[ASN][1000 genomes]
rs57854489	0.84[ASN][1000 genomes]
rs59620123	0.85[ASN][1000 genomes]
rs59850857	0.85[ASN][1000 genomes]
rs7137553	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7137876	0.92[EUR][1000 genomes]
rs7138458	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs721159	1.00[CHB][hapmap]
rs7303991	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs736310	0.85[ASN][1000 genomes]
rs758162	0.88[CEU][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs758163	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs758164	0.87[CEU][hapmap];0.93[EUR][1000 genomes]
rs758166	1.00[CHB][hapmap]
rs917367	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs917368	0.85[ASN][1000 genomes]
rs960671	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1963800-1965600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:1964000-1965200	ZNF genes & repeats	Brain Cingulate Gyrus	brain
3	chr12:1964200-1964800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:1964200-1965200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:1964400-1964800	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:1964400-1965000	ZNF genes & repeats	Aorta	Aorta
7	chr12:1964400-1965200	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr12:1964400-1965200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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