Variant report

Variant	rs3021373
Chromosome Location	chr5:52348367-52348368
allele	C/G
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: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10041086	0.91[YRI][hapmap]
rs10051425	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051483	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055919	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10058715	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065574	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065693	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1042324	0.80[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513009	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1139484	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13356629	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13357783	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1445940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880872	1.00[CEU][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16880873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880892	0.89[CEU][hapmap];0.83[AMR][1000 genomes]
rs1801106	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2193969	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2233214	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2287873	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303120	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303125	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28841614	0.81[EUR][1000 genomes]
rs2910966	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2974984	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212429	0.86[AFR][1000 genomes]
rs3212433	0.86[YRI][hapmap]
rs3212436	0.87[YRI][hapmap]
rs3212444	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212468	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212487	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212491	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212492	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212493	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212497	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212498	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212503	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212504	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212515	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3212526	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3212528	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212529	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212536	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212539	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212543	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212544	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3212545	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212546	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212548	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212558	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3212567	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212568	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212569	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212570	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3212573	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212579	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3212580	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212582	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212584	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212585	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3212586	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3212588	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3212593	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212606	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212607	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212612	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212613	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212615	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212628	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212633	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3212634	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212635	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3212643	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213805	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3797474	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797494	0.91[YRI][hapmap]
rs3797497	0.91[YRI][hapmap]
rs3815755	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7446448	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs7700416	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][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	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	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
4	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
5	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
6	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
7	nsv880600	chr5:52342760-52362765	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv880861	chr5:52347692-52362765	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
2	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
3	chr5:52333800-52348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
5	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr5:52334000-52360800	Weak transcription	Small Intestine	intestine
7	chr5:52334600-52348400	Weak transcription	Lung	lung
8	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
9	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:52337200-52353400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr5:52337400-52348800	Weak transcription	A549	lung
13	chr5:52337400-52355200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:52337400-52369000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:52337400-52370200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:52341200-52396400	Strong transcription	HMEC	breast
17	chr5:52341400-52348600	Weak transcription	Dnd41	blood
18	chr5:52341400-52359000	Weak transcription	NHDF-Ad	bronchial
19	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:52341800-52358800	Weak transcription	Osteobl	bone
21	chr5:52342000-52367200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr5:52342400-52363600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:52342600-52383800	Strong transcription	NHEK	skin
24	chr5:52343000-52348600	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:52343000-52359000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:52343200-52350800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:52343200-52351800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr5:52343200-52361800	Strong transcription	HepG2	liver
29	chr5:52343400-52350000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:52343400-52357200	Strong transcription	HUVEC	blood vessel
31	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
32	chr5:52344000-52348600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:52344000-52369200	Weak transcription	Pancreas	Pancrea
34	chr5:52344200-52356000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:52344400-52356400	Weak transcription	Esophagus	oesophagus
36	chr5:52344400-52356400	Weak transcription	Gastric	stomach
37	chr5:52345600-52350800	Strong transcription	Hela-S3	cervix
38	chr5:52346200-52349000	Weak transcription	Fetal Brain Male	brain
39	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:52346400-52349800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr5:52346600-52348400	Weak transcription	NHLF	lung
42	chr5:52346600-52369200	Weak transcription	Brain Angular Gyrus	brain
43	chr5:52347000-52353000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:52347200-52370000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr5:52347600-52387000	Weak transcription	Fetal Stomach	stomach
46	chr5:52347800-52349200	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr5:52347800-52349600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr5:52347800-52350200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:52347800-52369200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas

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