Variant report

Variant	rs3747519
Chromosome Location	chr3:46711135-46711136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10451990	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs11711100	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13080080	0.81[JPT][hapmap]
rs4683269	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442017	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6442019	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs6803988	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs6806400	0.90[JPT][hapmap]
rs7433347	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9810659	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs9868213	0.80[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv876739	chr3:46656980-46744966	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv876740	chr3:46656980-46748453	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv876741	chr3:46663372-46763839	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv516623	chr3:46680063-46852679	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv1804680	chr3:46704348-46869911	Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv876742	chr3:46705369-46763839	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	nsv536555	chr3:46706571-46817963	Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv536556	chr3:46706571-46849443	Genic enhancers Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv536557	chr3:46706571-46853434	Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	nsv10268	chr3:46707169-46736718	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
16	esv1797503	chr3:46708712-46760713	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3747519	LRRC2	cis	cerebellum	SCAN
rs3747519	C3orf39	cis	cerebellum	SCAN
rs3747519	ALS2CL	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46702800-46732400	Weak transcription	Psoas Muscle	Psoas
2	chr3:46703000-46711600	Weak transcription	Esophagus	oesophagus
3	chr3:46703000-46731600	Weak transcription	Hela-S3	cervix
4	chr3:46704200-46712400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:46705000-46711400	Weak transcription	HMEC	breast
6	chr3:46705400-46711800	Weak transcription	Adipose Nuclei	Adipose
7	chr3:46705400-46711800	Weak transcription	Placenta	Placenta
8	chr3:46705400-46712400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:46705400-46713400	Weak transcription	Colonic Mucosa	Colon
10	chr3:46705400-46715000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:46705400-46732600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:46705400-46734400	Weak transcription	Ovary	ovary
13	chr3:46705800-46714600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:46705800-46714800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:46705800-46717000	Weak transcription	Brain Anterior Caudate	brain
16	chr3:46706000-46717400	Weak transcription	Brain Angular Gyrus	brain
17	chr3:46706800-46712200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:46707200-46717000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:46708000-46716600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:46708000-46717200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:46708600-46712000	Weak transcription	Lung	lung
22	chr3:46709000-46712000	Weak transcription	Liver	Liver
23	chr3:46709000-46712400	Weak transcription	Gastric	stomach
24	chr3:46709200-46711200	Weak transcription	Right Ventricle	heart
25	chr3:46709200-46712200	Weak transcription	Pancreas	Pancrea
26	chr3:46709400-46712600	Weak transcription	Left Ventricle	heart
27	chr3:46709600-46711400	Weak transcription	Primary T cells from cord blood	blood
28	chr3:46709800-46711400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:46709800-46711400	Weak transcription	Spleen	Spleen
30	chr3:46710000-46711800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:46710000-46715000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:46710000-46722000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:46710200-46711400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:46710200-46711400	Weak transcription	Fetal Intestine Small	intestine
35	chr3:46710200-46711400	Weak transcription	NHEK	skin
36	chr3:46710200-46711800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:46710200-46722800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:46710400-46716800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:46710800-46711400	Enhancers	Right Atrium	heart
40	chr3:46710800-46711800	Weak transcription	Fetal Intestine Large	intestine
41	chr3:46710800-46712400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr3:46710800-46712400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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