Variant report

Variant	rs7788090
Chromosome Location	chr7:64343985-64343986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10225171	0.86[ASN][1000 genomes]
rs10240146	0.95[ASN][1000 genomes]
rs10279535	0.88[ASN][1000 genomes]
rs10949938	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11760270	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11760727	0.86[ASN][1000 genomes]
rs11773349	0.84[ASN][1000 genomes]
rs11983033	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1464927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1464928	0.86[ASN][1000 genomes]
rs1525809	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1880656	0.86[ASN][1000 genomes]
rs3763506	0.86[ASN][1000 genomes]
rs4273744	0.93[ASN][1000 genomes]
rs4392773	0.95[ASN][1000 genomes]
rs4518551	0.86[ASN][1000 genomes]
rs4717220	0.89[ASN][1000 genomes]
rs4718122	0.84[ASN][1000 genomes]
rs4718125	0.89[ASN][1000 genomes]
rs4718131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs55683815	0.82[ASN][1000 genomes]
rs55762657	0.81[EUR][1000 genomes]
rs55780785	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55887902	0.91[ASN][1000 genomes]
rs56004721	0.86[ASN][1000 genomes]
rs56075681	0.86[ASN][1000 genomes]
rs56214350	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56391048	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56785930	0.95[ASN][1000 genomes]
rs57570718	0.86[ASN][1000 genomes]
rs58676599	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59477017	0.84[ASN][1000 genomes]
rs59666562	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59954648	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60779365	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6460199	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs67686910	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961445	0.82[ASN][1000 genomes]
rs6976546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978473	0.82[ASN][1000 genomes]
rs72504855	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73126358	0.84[ASN][1000 genomes]
rs73126387	0.86[ASN][1000 genomes]
rs73130313	0.88[ASN][1000 genomes]
rs73130314	0.88[ASN][1000 genomes]
rs73132347	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73132368	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73132377	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137851	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73142749	0.82[ASN][1000 genomes]
rs7782095	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7784902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7805112	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7808498	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7810067	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2755057	chr7:63819849-64345822	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
4	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv1022042	chr7:64226499-64566945	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1026390	chr7:64240323-64414364	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
10	nsv1033291	chr7:64273434-64406276	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv508457	chr7:64286522-64391112	Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
12	esv1797468	chr7:64296309-64356050	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv888282	chr7:64299645-64511564	Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
14	nsv1018967	chr7:64318129-64380869	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	esv3506582	chr7:64323055-64563984	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	esv3506583	chr7:64323055-64563984	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	esv21367	chr7:64328624-64345129	Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	esv1818246	chr7:64328632-64344038	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv1019180	chr7:64329889-64512842	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
20	nsv888283	chr7:64343985-64511564	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7788090	CRCP	cis	cerebellum	SCAN
rs7788090	ZNF273	cis	cerebellum	SCAN
rs7788090	ZNF117	cis	cerebellum	SCAN
rs7788090	ZNF117	cis	parietal	SCAN
rs7788090	ASL	cis	cerebellum	SCAN
rs7788090	CRCP	cis	parietal	SCAN
rs7788090	ZNF273	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64341200-64344200	ZNF genes & repeats	Brain Germinal Matrix	brain
2	chr7:64341800-64344000	Active TSS	Colon Smooth Muscle	Colon
3	chr7:64341800-64344800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr7:64342200-64344000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr7:64342400-64344200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:64342400-64344200	Active TSS	Brain Cingulate Gyrus	brain
7	chr7:64342400-64344200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr7:64342400-64344400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:64342400-64344400	Bivalent/Poised TSS	NHEK	skin
10	chr7:64342600-64344000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr7:64342600-64344200	ZNF genes & repeats	Spleen	Spleen
12	chr7:64342600-64344400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr7:64342600-64344400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
14	chr7:64343200-64344000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:64343400-64344000	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr7:64343400-64344200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
17	chr7:64343600-64344000	Enhancers	Pancreas	Pancrea
18	chr7:64343600-64344600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
19	chr7:64343800-64344000	Active TSS	Brain Hippocampus Middle	brain
20	chr7:64343800-64344000	Flanking Active TSS	Rectal Smooth Muscle	rectum
21	chr7:64343800-64344000	Enhancers	Right Ventricle	heart
22	chr7:64343800-64344200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr7:64343800-64344400	Enhancers	Esophagus	oesophagus
24	chr7:64343800-64348200	Weak transcription	Right Atrium	heart
25	chr7:64343800-64348400	Weak transcription	Ovary	ovary
26	chr7:64343800-64348600	Weak transcription	Brain Anterior Caudate	brain
27	chr7:64343800-64348600	Weak transcription	Brain Substantia Nigra	brain
28	chr7:64343800-64348600	Weak transcription	Psoas Muscle	Psoas

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