Variant report

Variant	rs3212435
Chromosome Location	chr5:52337326-52337327
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52285122..52287993-chr5:52333837..52337640,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249899	Chromatin interaction
ENSG00000164171	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

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	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1445942	0.80[AMR][1000 genomes]
rs17298242	0.82[AMR][1000 genomes]
rs1900182	0.83[AMR][1000 genomes]
rs2075614	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2287950	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]
rs3212431	1.00[YRI][hapmap]
rs3212433	0.93[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3212436	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs3212446	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212483	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212537	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3212556	0.97[ASN][1000 genomes]
rs3212603	0.81[AMR][1000 genomes]
rs3212646	1.00[YRI][hapmap]
rs3776788	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776789	0.90[AFR][1000 genomes];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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357234	0.91[AFR][1000 genomes];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:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv881217	chr5:52334774-52341512	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3212435	ESM1	cis	parietal	SCAN
rs3212435	MOCS2	cis	lymphoblastoid	seeQTL
rs3212435	ITGA2	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 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	chr5:52333400-52341400	Strong transcription	HepG2	liver
7	chr5:52333800-52348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
9	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:52334000-52360800	Weak transcription	Small Intestine	intestine
11	chr5:52334400-52338000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:52334400-52348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:52334600-52337400	Weak transcription	Adipose Nuclei	Adipose
14	chr5:52334600-52343400	Weak transcription	Gastric	stomach
15	chr5:52334600-52348400	Weak transcription	Lung	lung
16	chr5:52334800-52343400	Weak transcription	Esophagus	oesophagus
17	chr5:52334800-52343800	Weak transcription	Brain Hippocampus Middle	brain
18	chr5:52334800-52343800	Weak transcription	Pancreas	Pancrea
19	chr5:52334800-52348000	Weak transcription	Brain Substantia Nigra	brain
20	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
21	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:52335200-52337800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:52335800-52338200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:52336000-52337800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:52336400-52337600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr5:52336400-52338800	Strong transcription	HMEC	breast
27	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:52336600-52337400	Active TSS	Primary hematopoietic stem cells	blood
29	chr5:52336600-52337400	Genic enhancers	NHEK	skin
30	chr5:52336800-52337400	Enhancers	Hela-S3	cervix
31	chr5:52337000-52337400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr5:52337000-52337400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr5:52337000-52337400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr5:52337000-52337400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:52337000-52337400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr5:52337000-52337400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr5:52337000-52337400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:52337000-52337400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:52337000-52337400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:52337000-52337400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:52337000-52337400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr5:52337000-52337400	Active TSS	Duodenum Mucosa	Duodenum
43	chr5:52337000-52337400	Enhancers	Fetal Kidney	kidney
44	chr5:52337000-52337400	Flanking Active TSS	GM12878-XiMat	blood
45	chr5:52337000-52337400	Flanking Active TSS	NHDF-Ad	bronchial
46	chr5:52337000-52337600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:52337000-52337600	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr5:52337000-52337600	Active TSS	Primary T cells fromperipheralblood	blood
49	chr5:52337000-52337600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:52337000-52337600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links