Variant report

Variant	rs3212483
Chromosome Location	chr5:52343901-52343902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52342580..52344559-chr5:52347867..52350544,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10041086	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]
rs11741738	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1445941	0.85[AMR][1000 genomes]
rs1445942	0.80[AMR][1000 genomes]
rs17298242	0.84[ASW][hapmap];0.85[LWK][hapmap];0.82[AMR][1000 genomes]
rs1900182	0.83[AMR][1000 genomes]
rs2075614	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2287950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303124	0.83[AMR][1000 genomes]
rs3212430	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3212433	0.93[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3212435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212436	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs3212446	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212537	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3212556	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3212603	0.81[AMR][1000 genomes]
rs3776788	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776789	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797494	0.92[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs3797497	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3797500	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357234	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716436	0.83[GIH][hapmap];0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv881359	chr5:52339114-52345868	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv881388	chr5:52339234-52375536	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv881477	chr5:52339843-52345868	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv881148	chr5:52341064-52346527	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv881599	chr5:52341359-52344610	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv880600	chr5:52342760-52362765	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3212483	MOCS2	cis	lymphoblastoid	seeQTL
rs3212483	ESM1	cis	parietal	SCAN
rs3212483	ITGA2	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 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	chr5:52333800-52348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
8	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:52334000-52360800	Weak transcription	Small Intestine	intestine
10	chr5:52334400-52348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:52334600-52348400	Weak transcription	Lung	lung
12	chr5:52334800-52348000	Weak transcription	Brain Substantia Nigra	brain
13	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
14	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:52337200-52353400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr5:52337400-52346400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr5:52337400-52348800	Weak transcription	A549	lung
19	chr5:52337400-52355200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:52337400-52369000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr5:52337400-52370200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:52338000-52348200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:52341200-52346400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr5:52341200-52396400	Strong transcription	HMEC	breast
25	chr5:52341400-52345800	Weak transcription	NH-A	brain
26	chr5:52341400-52346400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr5:52341400-52348600	Weak transcription	Dnd41	blood
28	chr5:52341400-52359000	Weak transcription	NHDF-Ad	bronchial
29	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:52341800-52347800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:52341800-52358800	Weak transcription	Osteobl	bone
32	chr5:52342000-52367200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:52342400-52363600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr5:52342600-52344600	Strong transcription	Hela-S3	cervix
35	chr5:52342600-52383800	Strong transcription	NHEK	skin
36	chr5:52343000-52348600	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:52343000-52359000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:52343200-52344400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:52343200-52344600	Strong transcription	NHLF	lung
40	chr5:52343200-52346800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:52343200-52350800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:52343200-52351800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:52343200-52361800	Strong transcription	HepG2	liver
44	chr5:52343400-52344400	Strong transcription	Esophagus	oesophagus
45	chr5:52343400-52344400	Strong transcription	Gastric	stomach
46	chr5:52343400-52350000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:52343400-52357200	Strong transcription	HUVEC	blood vessel
48	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
49	chr5:52343600-52348000	Weak transcription	Spleen	Spleen
50	chr5:52343800-52344000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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