Variant report

Variant	rs209390
Chromosome Location	chr10:43128880-43128881
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	chr10:43124209..43130093-chr10:43131977..43134761,6	K562	blood:
2	chr10:43125083..43130093-chr10:43132029..43136060,7	K562	blood:

Variant related genes	Relation type
ENSG00000272373	Chromatin interaction
ENSG00000196693	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11239614	0.89[ASN][1000 genomes]
rs11239615	0.89[ASN][1000 genomes]
rs11239762	1.00[CHB][hapmap]
rs11499092	0.89[ASN][1000 genomes]
rs11499093	0.89[ASN][1000 genomes]
rs11499095	0.89[ASN][1000 genomes]
rs12246683	1.00[CHB][hapmap]
rs12254233	1.00[CHB][hapmap]
rs12259795	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12262877	1.00[CHB][hapmap]
rs12264895	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13376880	1.00[CHB][hapmap]
rs1539295	1.00[CHB][hapmap]
rs17158044	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs1831915	0.89[ASN][1000 genomes]
rs1855444	1.00[JPT][hapmap]
rs1855450	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1855460	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs1889310	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs209375	0.94[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs209376	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs209377	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209380	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs209381	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs209385	1.00[CHB][hapmap]
rs209386	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209387	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209388	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209389	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs209391	1.00[CHB][hapmap]
rs209392	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs210221	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs210222	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs210236	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs210240	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs210259	0.81[ASN][1000 genomes]
rs210260	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs210263	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs210267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs210280	1.00[CEU][hapmap];0.93[MEX][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs210281	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210282	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210285	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs210299	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs210300	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35917885	0.89[ASN][1000 genomes]
rs3740329	0.94[CEU][hapmap];0.93[MEX][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4450129	1.00[CHB][hapmap]
rs549167	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs55766110	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs574720	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs603671	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630838	0.91[EUR][1000 genomes]
rs644175	0.86[EUR][1000 genomes]
rs6593345	0.89[ASN][1000 genomes]
rs6593349	0.89[ASN][1000 genomes]
rs68055	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs683538	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7072200	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7073731	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7076849	0.82[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs7088389	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7099013	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7893674	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7908362	1.00[CHB][hapmap]
rs7908372	1.00[CHB][hapmap]
rs7911186	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7919712	0.82[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817455	chr10:42607635-43151812	Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv895064	chr10:42783481-43243325	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
9	nsv469725	chr10:42965130-43178323	Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv482513	chr10:42965130-43178323	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
12	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	nsv975036	chr10:43090222-43132879	ZNF genes & repeats Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	esv2757381	chr10:43104068-43352995	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
15	esv34929	chr10:43116194-43329770	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs209390	ZNF33B	cis	Adipose Subcutaneous	GTEx
rs209390	ZNF33B	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43089800-43133000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr10:43089800-43133000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr10:43089800-43133000	Weak transcription	Right Ventricle	heart
4	chr10:43090800-43133000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr10:43091200-43132800	Weak transcription	Colon Smooth Muscle	Colon
6	chr10:43091400-43132400	Weak transcription	HMEC	breast
7	chr10:43091400-43132800	Weak transcription	Colonic Mucosa	Colon
8	chr10:43094400-43133200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:43101000-43133000	Weak transcription	NH-A	brain
10	chr10:43102000-43132000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:43106200-43132600	Weak transcription	Fetal Heart	heart
12	chr10:43107000-43133000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr10:43107400-43129000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr10:43108000-43133200	Weak transcription	Psoas Muscle	Psoas
15	chr10:43109000-43133200	Weak transcription	Aorta	Aorta
16	chr10:43111200-43133000	Weak transcription	Brain Hippocampus Middle	brain
17	chr10:43111600-43132800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr10:43116000-43130000	Weak transcription	Stomach Mucosa	stomach
19	chr10:43117600-43133000	Weak transcription	Brain Angular Gyrus	brain
20	chr10:43117800-43129000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr10:43118000-43129200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr10:43118200-43129600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr10:43118200-43133000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr10:43118200-43133000	Weak transcription	HSMM	muscle
25	chr10:43118200-43133000	Weak transcription	NHLF	lung
26	chr10:43118400-43130200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr10:43119600-43133200	Weak transcription	Gastric	stomach
28	chr10:43119800-43132400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr10:43119800-43132400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr10:43119800-43133000	Weak transcription	Brain Anterior Caudate	brain
31	chr10:43119800-43133000	Weak transcription	Brain Substantia Nigra	brain
32	chr10:43119800-43133000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr10:43119800-43133000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr10:43119800-43133200	Weak transcription	Spleen	Spleen
35	chr10:43120000-43129000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr10:43120000-43133000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr10:43120200-43129000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr10:43120200-43133000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr10:43121000-43129000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr10:43121000-43129800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr10:43121200-43129200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr10:43121800-43133000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:43122800-43129400	Weak transcription	Fetal Intestine Small	intestine
44	chr10:43122800-43130800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr10:43122800-43130800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr10:43123200-43129800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr10:43123200-43129800	Strong transcription	Primary B cells from cord blood	blood
48	chr10:43123400-43129000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr10:43123800-43130600	Weak transcription	Pancreas	Pancrea
50	chr10:43124200-43129000	Strong transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links