Variant report

Variant	rs6962595
Chromosome Location	chr7:19739448-19739449
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	chr7:19737218..19740997-chr7:19747742..19750274,4	K562	blood:
2	chr7:19737378..19739669-chr7:19751275..19753137,2	K562	blood:

Variant related genes	Relation type
ENSG00000105849	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12532153	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12536065	0.86[AMR][1000 genomes]
rs12667746	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3735617	0.90[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4591920	0.85[AMR][1000 genomes]
rs4620176	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59113291	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61223965	0.89[EUR][1000 genomes]
rs67120244	0.86[AMR][1000 genomes]
rs67568939	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67733453	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72591424	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72591428	0.82[ASN][1000 genomes]
rs73274029	0.83[AFR][1000 genomes]
rs9690344	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs992934	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018601	chr7:19272360-20008881	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1033223	chr7:19682192-20461375	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv538795	chr7:19682192-20461375	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv524807	chr7:19714156-19803925	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6962595	AGR3	cis	parietal	SCAN
rs6962595	SNX13	cis	parietal	SCAN
rs6962595	MACC1	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:19729400-19739800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr7:19729800-19745000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:19730400-19747400	Weak transcription	HSMMtube	muscle
4	chr7:19731000-19746000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:19731600-19746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:19732200-19743400	Weak transcription	Esophagus	oesophagus
7	chr7:19732400-19745400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:19732600-19747000	Weak transcription	Pancreas	Pancrea
9	chr7:19733000-19745600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:19733000-19747400	Weak transcription	Spleen	Spleen
11	chr7:19733800-19747000	Weak transcription	Osteobl	bone
12	chr7:19733800-19747400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:19734000-19739600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr7:19734000-19745600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr7:19734000-19746000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:19734000-19746600	Weak transcription	Fetal Lung	lung
17	chr7:19734200-19740000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:19734200-19746000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:19734200-19746800	Weak transcription	Psoas Muscle	Psoas
20	chr7:19734400-19747000	Weak transcription	Fetal Muscle Leg	muscle
21	chr7:19734400-19747400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr7:19734600-19746400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:19734800-19747000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:19734800-19748000	Weak transcription	Lung	lung
25	chr7:19735000-19740000	Strong transcription	Dnd41	blood
26	chr7:19735000-19741000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:19735200-19741200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr7:19735400-19740200	Strong transcription	Adipose Nuclei	Adipose
29	chr7:19735400-19741800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:19735400-19742400	Weak transcription	Fetal Kidney	kidney
31	chr7:19735400-19744600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr7:19735400-19746000	Weak transcription	Fetal Brain Female	brain
33	chr7:19735400-19746400	Weak transcription	HMEC	breast
34	chr7:19735400-19747000	Weak transcription	Right Ventricle	heart
35	chr7:19735400-19747200	Weak transcription	Fetal Heart	heart
36	chr7:19735600-19744000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr7:19735600-19745600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:19735600-19746800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr7:19735800-19746800	Weak transcription	Brain Angular Gyrus	brain
40	chr7:19735800-19747000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr7:19735800-19747000	Weak transcription	Small Intestine	intestine
42	chr7:19735800-19747000	Weak transcription	Thymus	Thymus
43	chr7:19735800-19747800	Weak transcription	Colonic Mucosa	Colon
44	chr7:19736000-19740600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:19736000-19746600	Weak transcription	Brain Hippocampus Middle	brain
46	chr7:19736000-19748000	Weak transcription	Gastric	stomach
47	chr7:19736200-19741200	Weak transcription	Aorta	Aorta
48	chr7:19736200-19741600	Weak transcription	Fetal Stomach	stomach
49	chr7:19736200-19747600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:19736400-19746600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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