Variant report

Variant	rs1880860
Chromosome Location	chr7:4119285-4119286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10229320	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10230707	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10242122	0.95[CEU][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11976431	1.00[CEU][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11977057	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11979803	0.81[CEU][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap]
rs11979859	0.85[JPT][hapmap]
rs12701396	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12701397	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12701399	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs12701400	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs12701401	0.83[CEU][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap]
rs12701404	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13223093	0.95[CEU][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13223305	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs13232652	0.85[JPT][hapmap]
rs13232922	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs13233532	0.83[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap]
rs13247783	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17134341	0.91[CEU][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2342501	0.86[CEU][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28610392	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35493503	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35639799	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35898917	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35944316	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36066771	0.81[EUR][1000 genomes]
rs4526264	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs4607516	0.85[JPT][hapmap]
rs58222948	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62438173	0.83[EUR][1000 genomes]
rs62439624	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6462577	0.82[MEX][hapmap]
rs6946647	0.85[JPT][hapmap]
rs6961563	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7784086	0.95[CEU][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7784114	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs7785691	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs7790901	0.95[CEU][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7791238	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7802118	0.91[CEU][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs7802807	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1025497	chr7:3905444-4176032	Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv538686	chr7:3905444-4176032	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv464274	chr7:3955516-4613607	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv464275	chr7:3955516-4613607	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv464276	chr7:3955516-4613607	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv464277	chr7:3955516-4613607	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv464278	chr7:3955516-4613607	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv605939	chr7:3955516-4613607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1019305	chr7:3991646-4276004	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1033687	chr7:4006020-4267871	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv538688	chr7:4006020-4267871	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv917252	chr7:4017819-4374090	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv527624	chr7:4027536-4424054	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv1022794	chr7:4063874-4137968	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv538689	chr7:4063874-4137968	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv869540	chr7:4063875-4302040	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv1028689	chr7:4078345-4166552	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv538690	chr7:4078345-4166552	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv1018462	chr7:4097676-4173613	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv1016507	chr7:4105420-4255439	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv538691	chr7:4105420-4255439	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	esv2755976	chr7:4116507-4207997	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	nsv518299	chr7:4116665-4286597	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1880860	C7orf70	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4088800-4129400	Weak transcription	Right Ventricle	heart
2	chr7:4103000-4125600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:4105200-4120200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr7:4107800-4120200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr7:4109600-4122000	Weak transcription	Esophagus	oesophagus
6	chr7:4110200-4129400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr7:4111400-4119600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr7:4112400-4130200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:4112600-4119600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:4113800-4120800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:4116200-4129200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr7:4117000-4119400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:4117800-4129400	Weak transcription	Fetal Intestine Small	intestine
14	chr7:4118000-4128600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:4118200-4120000	Weak transcription	Fetal Brain Female	brain
16	chr7:4118400-4119400	ZNF genes & repeats	Gastric	stomach
17	chr7:4118600-4120600	Weak transcription	Fetal Brain Male	brain
18	chr7:4118800-4119400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:4118800-4119800	Strong transcription	Pancreas	Pancrea
20	chr7:4118800-4128400	Weak transcription	Aorta	Aorta
21	chr7:4119000-4119600	Enhancers	Fetal Stomach	stomach
22	chr7:4119200-4119400	ZNF genes & repeats	Spleen	Spleen
23	chr7:4119200-4119800	Enhancers	Fetal Lung	lung
24	chr7:4119200-4120000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr7:4119200-4120400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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