Variant report

Variant	rs7580118
Chromosome Location	chr2:32398134-32398135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:32395858..32398697-chr2:32406981..32409057,2	K562	blood:
2	chr2:32397197..32398862-chr2:32406291..32408481,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11887441	0.89[JPT][hapmap]
rs11887458	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11895183	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895623	0.98[ASN][1000 genomes]
rs11903729	1.00[CHB][hapmap]
rs12990358	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12992916	1.00[ASW][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs12994869	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs13029716	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034933	1.00[CHD][hapmap]
rs17011740	1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs17011742	0.93[CHD][hapmap];0.82[MEX][hapmap]
rs34437462	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs35245684	0.87[AFR][1000 genomes]
rs35262968	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]
rs35560333	0.98[ASN][1000 genomes]
rs3769607	0.93[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs3851309	0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs58980266	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60386495	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60906113	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6543653	0.88[ASN][1000 genomes]
rs6719805	0.88[ASN][1000 genomes]
rs6726255	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[TSI][hapmap]
rs6733630	1.00[CHB][hapmap]
rs6757121	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs71446054	0.90[AFR][1000 genomes]
rs71446055	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71446056	0.94[AFR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72493393	0.82[ASN][1000 genomes]
rs72863973	0.88[ASN][1000 genomes]
rs72863977	0.89[ASN][1000 genomes]
rs7562388	1.00[CHB][hapmap]
rs7574910	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7598154	1.00[CHD][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7580118	CLIP4	cis	cerebellum	SCAN
rs7580118	SLC30A6	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32391400-32401800	Weak transcription	Spleen	Spleen
2	chr2:32391400-32402000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:32391400-32402000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:32391600-32401800	Weak transcription	Gastric	stomach
5	chr2:32391600-32402000	Weak transcription	Esophagus	oesophagus
6	chr2:32391600-32402800	Weak transcription	Lung	lung
7	chr2:32391600-32403400	Weak transcription	Aorta	Aorta
8	chr2:32391600-32406600	Weak transcription	Small Intestine	intestine
9	chr2:32391600-32409600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:32391600-32426400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:32391600-32452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:32391800-32400200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:32391800-32400200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:32391800-32401800	Weak transcription	Brain Substantia Nigra	brain
15	chr2:32391800-32409600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:32391800-32431400	Weak transcription	Stomach Mucosa	stomach
17	chr2:32391800-32453800	Weak transcription	Colonic Mucosa	Colon
18	chr2:32392000-32398200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:32392000-32401800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:32392000-32401800	Weak transcription	Brain Angular Gyrus	brain
21	chr2:32392000-32401800	Weak transcription	Fetal Stomach	stomach
22	chr2:32392000-32402000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:32392000-32402000	Weak transcription	Fetal Lung	lung
24	chr2:32392000-32402000	Weak transcription	Thymus	Thymus
25	chr2:32392000-32402200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:32392000-32403600	Weak transcription	Fetal Kidney	kidney
27	chr2:32392000-32403800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:32392000-32403800	Weak transcription	HSMMtube	muscle
29	chr2:32392000-32414600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:32392000-32435800	Weak transcription	NHLF	lung
31	chr2:32392200-32398400	Weak transcription	Fetal Intestine Small	intestine
32	chr2:32392200-32402000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:32392200-32402000	Weak transcription	Brain Germinal Matrix	brain
34	chr2:32392200-32402200	Weak transcription	Osteobl	bone
35	chr2:32392200-32403600	Weak transcription	HUVEC	blood vessel
36	chr2:32392200-32411600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr2:32392200-32422800	Weak transcription	Fetal Brain Male	brain
38	chr2:32392200-32445200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:32392400-32399000	Weak transcription	Fetal Heart	heart
40	chr2:32392400-32402000	Weak transcription	Pancreas	Pancrea
41	chr2:32392600-32400000	Weak transcription	NHDF-Ad	bronchial
42	chr2:32392800-32398400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:32392800-32400800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:32392800-32410000	Weak transcription	Hela-S3	cervix
45	chr2:32392800-32447600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:32393000-32399000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:32393000-32400400	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:32393000-32412400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:32393200-32402200	Weak transcription	Brain Hippocampus Middle	brain
50	chr2:32395400-32405600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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