Variant report

Variant	rs2255532
Chromosome Location	chr3:48624611-48624612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48622640-48624741	A549	lung:	n/a	n/a
2	POLR2A	chr3:48624364-48626951	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48608891..48611470-chr3:48623633..48625269,2	MCF-7	breast:
2	chr3:48624465..48626090-chr3:48634843..48637573,2	K562	blood:

Variant related genes	Relation type
COL7A1	TF binding region
ENSG00000114270	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1003649	0.82[CHB][hapmap]
rs10470687	0.82[CHD][hapmap]
rs13060933	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs13091944	0.81[CHB][hapmap]
rs13319651	0.82[CHB][hapmap]
rs17080289	0.82[CHB][hapmap]
rs2854394	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs6781283	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs6792156	0.82[CHB][hapmap]
rs9830581	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9843316	0.82[CHB][hapmap]
rs9878950	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9881877	0.82[CHB][hapmap];0.82[CHD][hapmap]

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	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv3811	chr3:48599180-48643809	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2255532	DUSP7	cis	cerebellum	SCAN
rs2255532	MAPKAPK3	cis	parietal	SCAN
rs2255532	C3orf18	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48596600-48626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:48599000-48632000	Weak transcription	Left Ventricle	heart
3	chr3:48599200-48630600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:48600600-48631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:48601000-48631000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:48601600-48631000	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:48601800-48633000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:48602000-48629400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:48602000-48633200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:48602200-48629400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:48603600-48630000	Strong transcription	Fetal Stomach	stomach
12	chr3:48603800-48628800	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr3:48603800-48630600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:48603800-48631800	Weak transcription	Gastric	stomach
15	chr3:48604000-48629400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:48604000-48631600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:48604000-48632000	Weak transcription	HSMMtube	muscle
18	chr3:48604400-48630000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:48604400-48631600	Weak transcription	HSMM	muscle
20	chr3:48604600-48630800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:48605000-48627400	Strong transcription	NHEK	skin
22	chr3:48606200-48627600	Strong transcription	HMEC	breast
23	chr3:48606800-48627000	Strong transcription	A549	lung
24	chr3:48610200-48631200	Strong transcription	Fetal Intestine Small	intestine
25	chr3:48610800-48626000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:48615200-48627200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:48615200-48629600	Weak transcription	Brain Substantia Nigra	brain
28	chr3:48615200-48632000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:48615200-48632200	Weak transcription	Brain Anterior Caudate	brain
30	chr3:48615400-48625600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:48617000-48631600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:48617200-48630200	Weak transcription	NHDF-Ad	bronchial
33	chr3:48618400-48627000	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:48618600-48625000	Strong transcription	Osteobl	bone
35	chr3:48620000-48634600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:48620000-48634600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:48620600-48630400	Weak transcription	Hela-S3	cervix
38	chr3:48621000-48628000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:48621200-48624800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:48621400-48628800	Weak transcription	Colonic Mucosa	Colon
41	chr3:48621400-48630800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:48621600-48626000	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr3:48621800-48627600	Weak transcription	Placenta	Placenta
44	chr3:48622200-48631000	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:48622800-48626600	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:48622800-48631000	Strong transcription	NHLF	lung
47	chr3:48622800-48631800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:48623000-48629000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:48623200-48624800	Strong transcription	NH-A	brain
50	chr3:48623200-48625400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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