Variant report

Variant	rs4766426
Chromosome Location	chr12:1964640-1964641
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

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

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:1964603-1964653	AG09309	skin:	n/a
2	chr12:1964603-1964653	T-47D	breast:	n/a
3	chr12:1964603-1964653	NT2-D1	testis:	n/a
4	chr12:1964603-1964653	ovcar-3	ovarian:	n/a
5	chr12:1964603-1964653	HepG2	liver:	n/a
6	chr12:1964603-1964653	NB4	blood:	n/a
7	chr12:1964603-1964653	Jurkat	blood:	n/a
8	chr12:1964603-1964653	NHBE	bronchial:	n/a
9	chr12:1964603-1964653	A549	lung:	n/a
10	chr12:1964603-1964653	HCPEpiC	choroid plexus:	n/a
11	chr12:1964603-1964653	HUVEC	blood vessel:	n/a
12	chr12:1964603-1964653	GM19239	blood:	n/a
13	chr12:1964603-1964653	HEK293	kidney:	embryo
14	chr12:1964603-1964653	HEEpiC	esophagus:	n/a
15	chr12:1964603-1964653	HRCEpiC	kidney:	n/a
16	chr12:1964603-1964653	Caco-2	colon:	n/a
17	chr12:1964603-1964653	Hepatocyte	liver:	n/a
18	chr12:1964603-1964653	PrEC	prostate:	n/a
19	chr12:1964603-1964653	AG09319	gingival:	n/a
20	chr12:1964603-1964653	GM12891	blood:	n/a
21	chr12:1964603-1964653	AG04450	lung:	fetal
22	chr12:1964603-1964653	GM06990	blood:	n/a
23	chr12:1964603-1964653	ProgFib	skin:	n/a
24	chr12:1964603-1964653	NHDF-neo	bronchial:	n/a
25	chr12:1964603-1964653	BJ	skin:	n/a
26	chr12:1964603-1964653	U87	brain:	n/a
27	chr12:1964603-1964653	HIPEpiC	eye:	n/a
28	chr12:1964603-1964653	GM12892	blood:	n/a
29	chr12:1964603-1964653	HCF	heart:	n/a
30	chr12:1964603-1964653	MCF10A-Er-Src	breast:	n/a
31	chr12:1964603-1964653	PFSK-1	brain:	n/a
32	chr12:1964603-1964653	HCT-116	colon:	n/a
33	chr12:1964603-1964653	HL-60	blood:	n/a
34	chr12:1964603-1964653	HAEpiC	amniotic membrane:	n/a
35	chr12:1964603-1964653	AG04449	skin:	fetal
36	chr12:1964603-1964653	HMEC	breast:	n/a
37	chr12:1964603-1964653	SKMC	muscle:	n/a
38	chr12:1964603-1964653	CMK	blood:	n/a
39	chr12:1964603-1964653	SAEC	small airway:	n/a
40	chr12:1964603-1964653	K562	blood:	n/a
41	chr12:1964603-1964653	IMR90	lung:	fetal
42	chr12:1964603-1964653	HCM	heart:	n/a
43	chr12:1964603-1964653	HRE	kidney:	n/a
44	chr12:1964603-1964653	HPAEpiC	pulmonary alveolar:	n/a
45	chr12:1964603-1964653	ECC-1	luminal epithelium:	n/a
46	chr12:1964603-1964653	Hela-S3	cervix:	n/a
47	chr12:1964603-1964653	GM12878	blood:	n/a
48	chr12:1964603-1964653	H1-hESC	embryonic stem cell:	embryo
49	chr12:1964603-1964653	RPTEC	kidney:	n/a
50	chr12:1964603-1964653	BE2_C	brain:	n/a

(count:1 , 50 per page) page: 1

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

No data

Variant related genes	Relation type
CACNA2D4	TF binding region
CACNA2D4	CpG island

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10161058	0.84[ASN][1000 genomes]
rs10161097	0.99[ASN][1000 genomes]
rs1076331	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774000	0.92[ASN][1000 genomes]
rs11062000	0.87[EUR][1000 genomes]
rs11062002	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11062003	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11062004	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11062005	0.87[EUR][1000 genomes]
rs11062006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11062007	0.87[EUR][1000 genomes]
rs11834934	0.81[ASN][1000 genomes]
rs12582053	0.84[ASN][1000 genomes]
rs16928837	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16928848	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860052	0.93[ASN][1000 genomes]
rs1860053	1.00[ASN][1000 genomes]
rs2286368	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286369	0.95[ASN][1000 genomes]
rs2286371	0.92[ASN][1000 genomes]
rs2286372	0.92[ASN][1000 genomes]
rs2286374	0.92[ASN][1000 genomes]
rs3815324	0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4363670	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4766425	0.92[ASN][1000 genomes]
rs57854489	0.91[ASN][1000 genomes]
rs59620123	0.92[ASN][1000 genomes]
rs59850857	0.92[ASN][1000 genomes]
rs72653429	0.81[ASN][1000 genomes]
rs736310	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs758162	0.94[ASN][1000 genomes]
rs758163	0.92[ASN][1000 genomes]
rs7967890	0.87[EUR][1000 genomes]
rs917367	1.00[ASN][1000 genomes]
rs917368	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs960671	0.92[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:9 , 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
9	chr12:1964600-1965800	ZNF genes & repeats	Stomach Smooth Muscle	stomach

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