Variant report

Variant	rs323565
Chromosome Location	chr5:40848803-40848804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40833178..40835128-chr5:40848248..40850969,2	MCF-7	breast:
2	chr5:40827337..40829138-chr5:40847106..40849320,2	MCF-7	breast:
3	chr5:40847291..40849626-chr5:40854457..40858364,3	K562	blood:
4	chr5:40843666..40846372-chr5:40846627..40850268,4	K562	blood:
5	chr5:40834549..40837244-chr5:40846032..40850284,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145592	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1376178	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs1697938	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2122569	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs2443035	0.86[JPT][hapmap]
rs2459465	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs2597746	0.86[JPT][hapmap]
rs364443	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs420220	0.80[ASN][1000 genomes]
rs438652	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs441073	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6861054	0.80[ASN][1000 genomes]
rs6887212	0.80[ASN][1000 genomes]
rs837383	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs837388	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
2	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases
3	nsv820142	chr5:40847391-40852348	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs323565	DAB2	cis	cerebellum	SCAN
rs323565	C1orf146	trans	cerebellum	SCAN
rs323565	TTC33	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40836000-40852600	Weak transcription	Small Intestine	intestine
2	chr5:40841400-40852000	Weak transcription	Pancreas	Pancrea
3	chr5:40841800-40852400	Weak transcription	Esophagus	oesophagus
4	chr5:40842200-40852200	Weak transcription	Left Ventricle	heart
5	chr5:40842200-40852600	Weak transcription	Placenta	Placenta
6	chr5:40842200-40853800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:40842400-40852000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:40842400-40852400	Weak transcription	Liver	Liver
9	chr5:40842400-40852400	Weak transcription	Ovary	ovary
10	chr5:40842400-40852600	Weak transcription	Primary T cells from cord blood	blood
11	chr5:40842400-40853400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:40842400-40853800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:40842400-40854200	Weak transcription	Fetal Stomach	stomach
14	chr5:40842400-40854600	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:40842800-40849000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:40842800-40849200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:40842800-40852000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr5:40842800-40853200	Weak transcription	Fetal Intestine Small	intestine
19	chr5:40842800-40854000	Weak transcription	Aorta	Aorta
20	chr5:40842800-40856000	Weak transcription	Right Ventricle	heart
21	chr5:40843000-40849000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:40843200-40852200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:40843400-40851800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:40843400-40852400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:40843600-40854000	Weak transcription	Colon Smooth Muscle	Colon
26	chr5:40843600-40857800	Weak transcription	Osteobl	bone
27	chr5:40843800-40852000	Weak transcription	Adipose Nuclei	Adipose
28	chr5:40843800-40852000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:40844000-40852200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:40844000-40852400	Weak transcription	Hela-S3	cervix
31	chr5:40845400-40851400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:40845400-40852400	Weak transcription	Gastric	stomach
33	chr5:40846800-40849400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr5:40846800-40851800	Weak transcription	Lung	lung
35	chr5:40846800-40852000	Weak transcription	Spleen	Spleen
36	chr5:40846800-40852400	Weak transcription	HUVEC	blood vessel
37	chr5:40847000-40849000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr5:40847200-40849200	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr5:40847400-40849000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr5:40847400-40849400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:40848800-40849800	Enhancers	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links