Variant report

Variant	rs71309963
Chromosome Location	chr3:56601044-56601045
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56590931..56593644-chr3:56601004..56602846,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPATA12-5	chr3:56600978-56601081	NONHSAT090053
2	lnc-SPATA12-5	chr3:56600811-56601081	NONHSAT090054
3	lnc-SPATA12-5	chr3:56600979-56601081	NONHSAT090055

Variant related genes	Relation type
ENSG00000180376	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs13060656	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13068670	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072654	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13074639	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13080003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13086565	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13088166	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13089169	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13089332	0.93[EUR][1000 genomes]
rs13090343	0.84[ASN][1000 genomes]
rs13095165	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17825529	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1826119	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34097767	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34171578	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34284682	0.89[EUR][1000 genomes]
rs34349699	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34480364	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34720351	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34869541	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34885435	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34911835	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34953718	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35070694	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35286628	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35418695	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35564119	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35677810	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35689307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35728519	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35785755	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35803417	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35940731	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35995233	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36029237	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36064180	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36131262	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732506	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4060982	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4538344	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4635676	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6807338	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71309961	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs71309962	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs71309964	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71309965	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71309970	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71309972	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71309973	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71309975	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71621834	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7431634	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:56592400-56601200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:56592400-56601400	Weak transcription	Left Ventricle	heart
5	chr3:56592400-56601800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:56592400-56601800	Weak transcription	Lung	lung
7	chr3:56592400-56602000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:56592400-56602800	Weak transcription	Esophagus	oesophagus
9	chr3:56592400-56602800	Weak transcription	Gastric	stomach
10	chr3:56592400-56602800	Weak transcription	Spleen	Spleen
11	chr3:56592400-56603000	Weak transcription	Pancreas	Pancrea
12	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
13	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
15	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
16	chr3:56592600-56601800	Weak transcription	Aorta	Aorta
17	chr3:56592600-56602200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:56592600-56602200	Weak transcription	Brain Germinal Matrix	brain
19	chr3:56592600-56602200	Weak transcription	Fetal Brain Male	brain
20	chr3:56592600-56603000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:56592600-56603800	Weak transcription	Stomach Mucosa	stomach
22	chr3:56592800-56602000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:56592800-56602000	Weak transcription	Brain Angular Gyrus	brain
24	chr3:56592800-56602000	Weak transcription	A549	lung
25	chr3:56592800-56610200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
27	chr3:56593000-56602200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:56593000-56603000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:56593000-56607800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:56593000-56610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:56593200-56602000	Weak transcription	Brain Substantia Nigra	brain
32	chr3:56593200-56608000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:56593200-56609000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:56593200-56609600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:56593200-56616400	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:56593400-56602400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr3:56593400-56607600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:56593400-56608600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:56593600-56609800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:56594000-56603000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:56594200-56602000	Strong transcription	HUVEC	blood vessel
42	chr3:56594200-56608000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:56594200-56610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:56594400-56609400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:56594800-56604000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr3:56594800-56609000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:56595400-56602000	Weak transcription	Brain Anterior Caudate	brain
48	chr3:56596000-56602200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:56596000-56605800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr3:56596000-56608400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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