Variant report

Variant	rs3212424
Chromosome Location	chr5:52323453-52323454
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52284308..52287113-chr5:52321640..52324132,2	MCF-7	breast:
2	chr17:62236129..62238534-chr5:52321834..52323811,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249899	Chromatin interaction
ENSG00000164171	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10940290	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11959632	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12521915	0.83[CEU][hapmap]
rs12652168	0.81[EUR][1000 genomes]
rs12657429	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12657501	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12657972	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12657980	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1316250	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1363192	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1421937	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1445943	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16880627	0.83[JPT][hapmap]
rs16880669	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1862191	0.83[EUR][1000 genomes]
rs2303122	0.83[CEU][hapmap]
rs3212438	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3212439	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3212441	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3212450	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3212453	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3212455	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3212457	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3212458	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3212461	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3212464	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3212467	0.83[EUR][1000 genomes]
rs3212472	0.82[EUR][1000 genomes]
rs3212478	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3212480	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3212481	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3212486	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3756537	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3776787	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3797495	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3797496	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3797498	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3822558	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3926397	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62357232	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62357233	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67719154	0.82[EUR][1000 genomes]
rs6880055	0.82[CEU][hapmap]
rs7705328	0.81[YRI][hapmap]
rs989073	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3212424	ITGA2	cis	multi-tissue	Pritchard
rs3212424	ISL1	cis	cerebellum	SCAN
rs3212424	MOCS2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52307000-52333800	Weak transcription	Gastric	stomach
2	chr5:52314200-52328600	Weak transcription	Lung	lung
3	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:52314400-52326200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:52317200-52327200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:52317400-52326800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:52317600-52326800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:52317600-52333600	Weak transcription	Colonic Mucosa	Colon
9	chr5:52318400-52331800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:52318800-52327200	Genic enhancers	HMEC	breast
11	chr5:52319000-52325400	Enhancers	Brain Substantia Nigra	brain
12	chr5:52319200-52325400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:52319200-52326200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:52319200-52327600	Weak transcription	Fetal Intestine Large	intestine
15	chr5:52319600-52326600	Weak transcription	Small Intestine	intestine
16	chr5:52320600-52323600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:52320600-52326200	Weak transcription	Esophagus	oesophagus
18	chr5:52320600-52327400	Weak transcription	HSMM	muscle
19	chr5:52320600-52327600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:52321000-52323600	Weak transcription	NHDF-Ad	bronchial
21	chr5:52321000-52326600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:52321600-52323600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:52321600-52326800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr5:52321800-52326000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr5:52321800-52326800	Weak transcription	Fetal Lung	lung
26	chr5:52322200-52326400	Genic enhancers	HepG2	liver
27	chr5:52322200-52333200	Weak transcription	Fetal Stomach	stomach
28	chr5:52322400-52324800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr5:52322600-52326400	Weak transcription	Fetal Kidney	kidney
30	chr5:52322800-52324000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:52323000-52324600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr5:52323000-52324600	Enhancers	HUVEC	blood vessel
33	chr5:52323000-52324800	Enhancers	Brain Hippocampus Middle	brain
34	chr5:52323000-52326400	Genic enhancers	Hela-S3	cervix
35	chr5:52323000-52327000	Enhancers	A549	lung
36	chr5:52323000-52327200	Genic enhancers	NHEK	skin
37	chr5:52323200-52323800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:52323200-52324400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:52323200-52324400	Enhancers	Brain Angular Gyrus	brain
40	chr5:52323200-52324400	Enhancers	Brain Anterior Caudate	brain
41	chr5:52323200-52324800	Enhancers	Brain Cingulate Gyrus	brain
42	chr5:52323200-52324800	Enhancers	NH-A	brain
43	chr5:52323200-52326400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:52323200-52326400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:52323200-52327000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:52323200-52329000	Enhancers	NHLF	lung
47	chr5:52323400-52323600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr5:52323400-52323600	Enhancers	Stomach Smooth Muscle	stomach
49	chr5:52323400-52323800	Enhancers	Pancreas	Pancrea
50	chr5:52323400-52324000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links