Variant report

Variant	rs13094371
Chromosome Location	chr3:93842702-93842703
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11927165	0.87[ASN][1000 genomes]
rs13095871	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054081	1.00[EUR][1000 genomes]
rs28372461	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs28479320	0.87[ASN][1000 genomes]
rs34814018	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6765330	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs7615950	1.00[CHD][hapmap]
rs7644176	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs9810986	0.87[ASN][1000 genomes]
rs9860824	0.93[EUR][1000 genomes]
rs9867629	1.00[EUR][1000 genomes]
rs9869941	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9879796	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats 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 miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription 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 target site	23 gene(s)	inside rSNPs	diseases
4	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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 miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv1795060	chr3:93602038-93848525	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
8	esv1791740	chr3:93602927-93849247	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
9	esv2755326	chr3:93605126-93882750	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	n/a
10	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv877162	chr3:93779664-94278078	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv877163	chr3:93795972-94047775	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13094371	NECAP2	trans	lymphoblastoid	seeQTL
rs13094371	NETO2	trans	lymphoblastoid	seeQTL
rs13094371	MRPS5	trans	lymphoblastoid	seeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93782800-93848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:93782800-93849400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:93783200-93851600	Weak transcription	HMEC	breast
4	chr3:93786800-93849800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:93795600-93847000	Weak transcription	Osteobl	bone
6	chr3:93796000-93857800	Weak transcription	Fetal Brain Male	brain
7	chr3:93799000-93851600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:93800200-93851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:93802400-93849600	Weak transcription	Stomach Mucosa	stomach
10	chr3:93802600-93851800	Weak transcription	Small Intestine	intestine
11	chr3:93808400-93849600	Weak transcription	Fetal Heart	heart
12	chr3:93812400-93852200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:93814600-93845200	Weak transcription	Esophagus	oesophagus
14	chr3:93814600-93847000	Weak transcription	Spleen	Spleen
15	chr3:93814600-93849400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:93814600-93849400	Weak transcription	Right Ventricle	heart
17	chr3:93814600-93849600	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:93814600-93849800	Weak transcription	Colonic Mucosa	Colon
19	chr3:93814800-93845200	Weak transcription	Gastric	stomach
20	chr3:93814800-93857800	Weak transcription	Pancreas	Pancrea
21	chr3:93815600-93848400	Weak transcription	Placenta	Placenta
22	chr3:93817200-93844800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:93817400-93849600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:93817600-93847000	Weak transcription	HepG2	liver
25	chr3:93817600-93848000	Weak transcription	NH-A	brain
26	chr3:93817800-93843000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:93817800-93846000	Weak transcription	Brain Angular Gyrus	brain
28	chr3:93817800-93848000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:93818000-93850200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:93818600-93843200	Weak transcription	Aorta	Aorta
31	chr3:93818600-93847000	Weak transcription	Lung	lung
32	chr3:93819400-93844800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:93819400-93850400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:93823000-93845600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:93823600-93849800	Weak transcription	HSMMtube	muscle
36	chr3:93823600-93857600	Weak transcription	Fetal Brain Female	brain
37	chr3:93824800-93845200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:93825400-93848000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:93826400-93843000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:93826400-93844600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:93826400-93844800	Weak transcription	Fetal Stomach	stomach
42	chr3:93826400-93851800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:93826800-93851400	Weak transcription	Hela-S3	cervix
44	chr3:93828800-93856000	Weak transcription	HSMM	muscle
45	chr3:93831200-93844600	Weak transcription	Thymus	Thymus
46	chr3:93831400-93843600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:93831400-93844600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:93831600-93843200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:93831600-93844600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:93831600-93844800	Weak transcription	Fetal Muscle Leg	muscle

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