Variant report

Variant	rs2707466
Chromosome Location	chr7:120979089-120979090
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	chr7:120960951..120962790-chr7:120977228..120979888,2	K562	blood:
2	chr7:120978814..120981059-chr7:121187814..121189792,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2244812	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254595	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2270215	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2536172	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2536180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2536182	0.92[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2536185	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2536189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779381	0.90[JPT][hapmap]
rs3801387	0.90[JPT][hapmap]
rs4727924	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs718766	0.90[JPT][hapmap]
rs7776725	0.90[JPT][hapmap]
rs7793554	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7807894	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs917726	0.90[JPT][hapmap]
rs917727	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
2	nsv1034353	chr7:120818382-121040576	Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1026322	chr7:120841937-121188037	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv539102	chr7:120841937-121188037	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2755350	chr7:120848049-121119049	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv2757237	chr7:120908459-120993326	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	esv2759558	chr7:120908459-120993326	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv1032054	chr7:120926379-121432971	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv539103	chr7:120926379-121432971	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Cortical thickness	22792071	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2707466	HYAL4	cis	cerebellum	SCAN
rs2707466	FAM3C	Cis_1M	lymphoblastoid	RTeQTL
rs2707466	ASZ1	cis	parietal	SCAN
rs2707466	GK2	trans	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120970600-121016800	Weak transcription	Gastric	stomach
2	chr7:120970600-121025400	Weak transcription	Spleen	Spleen
3	chr7:120970800-120979200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:120970800-120982600	Weak transcription	HSMM	muscle
5	chr7:120970800-121000400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:120971000-120986400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:120972000-120982000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr7:120972000-120986600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:120972000-120992400	Weak transcription	Esophagus	oesophagus
10	chr7:120973800-120998800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr7:120974600-120981800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:120974800-120986400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:120975600-120992400	Weak transcription	HSMMtube	muscle
14	chr7:120975800-120979200	Weak transcription	Aorta	Aorta
15	chr7:120975800-120984000	Weak transcription	NHLF	lung
16	chr7:120976000-120982000	Weak transcription	Primary B cells from cord blood	blood
17	chr7:120976400-120986200	Weak transcription	NHEK	skin
18	chr7:120976400-120986800	Weak transcription	Fetal Brain Female	brain
19	chr7:120977000-120985600	Weak transcription	Left Ventricle	heart
20	chr7:120977400-120984800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr7:120977400-120987000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:120977600-120992400	Weak transcription	Fetal Intestine Small	intestine
23	chr7:120977800-120982200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:120977800-120985800	Weak transcription	Primary T cells from cord blood	blood
25	chr7:120977800-120986600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:120977800-120999800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr7:120978000-120984000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr7:120978000-120986400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:120978200-120982200	Weak transcription	NHDF-Ad	bronchial
30	chr7:120978200-120984800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr7:120978400-120979200	Weak transcription	Lung	lung
32	chr7:120978400-120982000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:120978600-120979200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr7:120978600-120986800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:120978600-120990600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr7:120978600-120994600	Weak transcription	Fetal Thymus	thymus
37	chr7:120978800-120979600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:120978800-121017400	Weak transcription	Brain Inferior Temporal Lobe	brain

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