Variant report

Variant	rs6747410
Chromosome Location	chr2:98866775-98866776
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	chr2:98611658..98614514-chr2:98866353..98868181,2	K562	blood:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10172281	0.83[ASN][1000 genomes]
rs10181000	1.00[CHB][hapmap]
rs10190679	0.93[EUR][1000 genomes]
rs10199476	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs10202618	0.81[ASN][1000 genomes]
rs10203437	0.81[ASN][1000 genomes]
rs10210685	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11124096	0.87[CHB][hapmap]
rs11124107	0.87[CHB][hapmap]
rs11124119	0.83[ASN][1000 genomes]
rs11124121	0.81[ASN][1000 genomes]
rs11673807	0.87[CHB][hapmap]
rs11679920	0.87[CHB][hapmap]
rs11889349	0.87[CHB][hapmap]
rs11895654	0.87[CHB][hapmap]
rs11901562	0.87[ASN][1000 genomes]
rs12478763	0.87[CHB][hapmap]
rs12622324	0.87[CHB][hapmap]
rs12712256	0.87[ASN][1000 genomes]
rs12999985	0.87[CHB][hapmap]
rs13014142	0.87[CHB][hapmap]
rs13394706	1.00[CHB][hapmap]
rs13408372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs13428221	0.87[ASN][1000 genomes]
rs13432099	0.90[EUR][1000 genomes]
rs1451251	0.93[CHB][hapmap]
rs1466944	0.87[CHB][hapmap]
rs1504679	0.81[ASN][1000 genomes]
rs17427684	0.81[ASN][1000 genomes]
rs17429208	1.00[CHB][hapmap]
rs1875880	0.81[ASN][1000 genomes]
rs2102270	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs2122756	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs2202387	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs2221416	0.87[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs2292118	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2292119	0.87[CHB][hapmap]
rs3769755	0.80[CHB][hapmap]
rs4374424	0.87[CHB][hapmap]
rs4389366	0.87[ASN][1000 genomes]
rs4455212	0.92[CHB][hapmap]
rs4477970	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs4479470	0.87[CHB][hapmap]
rs4608580	0.87[CHB][hapmap]
rs4614979	0.83[ASN][1000 genomes]
rs4632400	0.87[CHB][hapmap]
rs4851122	0.87[ASN][1000 genomes]
rs4851123	0.81[ASN][1000 genomes]
rs4851935	0.87[CHB][hapmap]
rs4851951	0.92[CHB][hapmap]
rs4851953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851954	0.85[ASN][1000 genomes]
rs4851955	0.81[ASN][1000 genomes]
rs56320609	0.83[ASN][1000 genomes]
rs60924437	0.80[ASN][1000 genomes]
rs62156263	0.80[ASN][1000 genomes]
rs62156264	0.80[ASN][1000 genomes]
rs6543419	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs6715989	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs6725543	0.87[CHB][hapmap];0.84[CHD][hapmap]
rs6747344	0.87[CHB][hapmap]
rs6754222	0.93[CHB][hapmap]
rs72819909	0.81[ASN][1000 genomes]
rs72950941	0.89[ASN][1000 genomes]
rs7578802	0.87[CHB][hapmap]
rs7598554	0.87[ASN][1000 genomes]
rs7601049	0.87[CHB][hapmap]
rs7606070	0.81[ASN][1000 genomes]
rs7606220	0.87[CHB][hapmap]
rs937726	0.81[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	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv582513	chr2:98829237-98869914	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv582514	chr2:98835962-98869914	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1014147	chr2:98855007-98878044	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv818075	chr2:98855497-98872039	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv582515	chr2:98855497-98885925	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv517669	chr2:98855497-98889961	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv437289	chr2:98855497-98891519	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3459702	chr2:98856083-98886708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv3459703	chr2:98856205-98886602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv19987	chr2:98856422-98886491	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv1010376	chr2:98858308-98878044	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv1008771	chr2:98858308-98881340	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	esv2760564	chr2:98858308-98881352	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv1012433	chr2:98858308-98888391	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv1012121	chr2:98858308-98889961	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv1005509	chr2:98860142-98878044	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	nsv1003683	chr2:98860536-98881340	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	nsv999884	chr2:98861412-98881340	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	esv3693390	chr2:98862097-98886666	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6747410	CNGA3	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98865200-98870000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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