Variant report

Variant	rs3212441
Chromosome Location	chr5:52337908-52337909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10940290	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1126643	0.81[ASW][hapmap];0.87[YRI][hapmap]
rs11959632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521915	0.83[CEU][hapmap];0.83[YRI][hapmap]
rs12652168	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12657429	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12657501	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12657972	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12657980	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1316250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1363192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1445943	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16880669	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1862191	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2303122	0.83[CEU][hapmap]
rs2303127	0.80[AFR][1000 genomes]
rs3212424	1.00[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3212438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212450	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212453	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212455	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212457	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212458	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212464	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212467	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3212472	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3212478	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212480	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212481	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212486	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756537	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3776787	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3797495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822558	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3926397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357232	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62357233	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67719154	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6880055	0.82[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7725246	0.83[YRI][hapmap]
rs989073	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv880389	chr5:52333420-52375199	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv881217	chr5:52334774-52341512	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv881071	chr5:52334774-52362765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3212441	ISL1	cis	cerebellum	SCAN
rs3212441	MOCS2	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
3	chr5:52327800-52344200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
5	chr5:52328800-52348000	Weak transcription	Fetal Intestine Large	intestine
6	chr5:52333400-52341400	Strong transcription	HepG2	liver
7	chr5:52333800-52348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
9	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:52334000-52360800	Weak transcription	Small Intestine	intestine
11	chr5:52334400-52338000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:52334400-52348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:52334600-52343400	Weak transcription	Gastric	stomach
14	chr5:52334600-52348400	Weak transcription	Lung	lung
15	chr5:52334800-52343400	Weak transcription	Esophagus	oesophagus
16	chr5:52334800-52343800	Weak transcription	Brain Hippocampus Middle	brain
17	chr5:52334800-52343800	Weak transcription	Pancreas	Pancrea
18	chr5:52334800-52348000	Weak transcription	Brain Substantia Nigra	brain
19	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
20	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:52335800-52338200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:52336400-52338800	Strong transcription	HMEC	breast
23	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:52337000-52338000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:52337000-52338000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:52337000-52338000	Enhancers	Brain Cingulate Gyrus	brain
27	chr5:52337000-52340800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:52337200-52353400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:52337400-52338000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr5:52337400-52338000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr5:52337400-52338200	Enhancers	Primary hematopoietic stem cells	blood
32	chr5:52337400-52338400	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr5:52337400-52338400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:52337400-52339000	Strong transcription	NHEK	skin
35	chr5:52337400-52340200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:52337400-52340600	Weak transcription	Hela-S3	cervix
37	chr5:52337400-52340600	Weak transcription	Osteobl	bone
38	chr5:52337400-52340800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr5:52337400-52346400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr5:52337400-52348800	Weak transcription	A549	lung
41	chr5:52337400-52355200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:52337400-52369000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:52337400-52370200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:52337600-52338200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr5:52337600-52338200	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr5:52337600-52338200	Strong transcription	HUVEC	blood vessel
47	chr5:52337600-52338400	Enhancers	Dnd41	blood
48	chr5:52337600-52338400	Weak transcription	NHLF	lung
49	chr5:52337600-52340600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:52337600-52340800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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