Variant report

Variant	rs333692
Chromosome Location	chr10:20129463-20129464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10764159	0.87[EUR][1000 genomes]
rs10764164	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10827885	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12257233	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1590963	0.81[ASN][1000 genomes]
rs1977539	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2481936	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2481937	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2481938	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2481939	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2884470	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs333687	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs333689	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs333691	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs420898	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs442830	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs447706	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4748612	0.89[ASN][1000 genomes]
rs6482065	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7086438	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7094033	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7906452	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7908480	0.88[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7911243	0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7912855	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7914865	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7914996	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7922577	0.87[MEX][hapmap]
rs989767	0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049295	chr10:19740296-20509036	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1044794	chr10:20010269-20391329	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv540510	chr10:20010269-20391329	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1038966	chr10:20010469-20391190	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv540511	chr10:20010469-20391190	Enhancers Flanking Active TSS Weak transcription Strong transcription 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	7 gene(s)	inside rSNPs	diseases
6	nsv1037055	chr10:20010469-20651965	Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv540512	chr10:20010469-20651965	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:20110400-20151400	Weak transcription	Fetal Intestine Small	intestine
2	chr10:20115200-20154000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr10:20118200-20136200	Weak transcription	Colon Smooth Muscle	Colon
4	chr10:20122200-20132600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr10:20122400-20131200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr10:20122400-20132600	Weak transcription	Psoas Muscle	Psoas
7	chr10:20122400-20133600	Weak transcription	Left Ventricle	heart
8	chr10:20122600-20131400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr10:20122600-20136000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:20122800-20149000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr10:20126200-20142600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr10:20126400-20132600	Weak transcription	Fetal Stomach	stomach
13	chr10:20126600-20131200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr10:20126600-20132400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr10:20126800-20130000	Weak transcription	Brain Hippocampus Middle	brain
16	chr10:20127000-20130800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr10:20128200-20130200	Enhancers	Brain Substantia Nigra	brain
18	chr10:20128200-20134000	Weak transcription	Right Atrium	heart
19	chr10:20128400-20130000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr10:20128400-20132600	Weak transcription	Aorta	Aorta
21	chr10:20128400-20133400	Enhancers	Fetal Lung	lung
22	chr10:20128400-20145200	Weak transcription	Small Intestine	intestine
23	chr10:20128600-20132000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr10:20128600-20132600	Weak transcription	Brain Angular Gyrus	brain
25	chr10:20128600-20134200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr10:20128800-20130800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr10:20128800-20131600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr10:20129000-20131200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr10:20129000-20131400	Weak transcription	Brain Anterior Caudate	brain
30	chr10:20129000-20132200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr10:20129000-20134200	Weak transcription	Fetal Kidney	kidney
32	chr10:20129200-20131200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr10:20129200-20131400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr10:20129200-20131600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr10:20129200-20132000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr10:20129200-20132600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr10:20129200-20132600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr10:20129400-20131800	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links