Variant report

Variant	rs2276606
Chromosome Location	chr2:20069414-20069415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20066730..20071387-chr2:20098933..20103374,5	MCF-7	breast:
2	chr2:20066412..20068865-chr2:20069307..20071942,2	MCF-7	breast:
3	chr2:20068233..20072834-chr2:20097586..20102817,5	K562	blood:

Variant related genes	Relation type
ENSG00000183891	Chromatin interaction
ENSG00000228784	Chromatin interaction
ENSG00000271991	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2276607	0.86[LWK][hapmap]
rs7566585	0.81[CEU][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9306887	0.81[CEU][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]

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	nsv873711	chr2:19950864-20073860	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
4	nsv455819	chr2:19987440-20095690	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv581155	chr2:19987440-20095690	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv873714	chr2:20019616-20113088	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
7	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2276606	MSGN1	cis	parietal	SCAN
rs2276606	PHF17	trans	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20063600-20070600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:20068200-20069600	Flanking Active TSS	Fetal Thymus	thymus
3	chr2:20068400-20069600	Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr2:20068800-20069600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr2:20068800-20069800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr2:20068800-20075600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:20068800-20086200	Weak transcription	Spleen	Spleen
8	chr2:20068800-20097200	Weak transcription	Aorta	Aorta
9	chr2:20069000-20069600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:20069000-20069600	Enhancers	Lung	lung
11	chr2:20069000-20069800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:20069000-20069800	Enhancers	GM12878-XiMat	blood
13	chr2:20069000-20098200	Weak transcription	Right Atrium	heart
14	chr2:20069200-20069600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:20069200-20069600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr2:20069200-20069600	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr2:20069200-20069600	Flanking Active TSS	Thymus	Thymus
18	chr2:20069200-20069800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:20069200-20070200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:20069200-20072800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:20069200-20077600	Weak transcription	Fetal Lung	lung
22	chr2:20069400-20069600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:20069400-20069600	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr2:20069400-20069600	Enhancers	Gastric	stomach
25	chr2:20069400-20069600	Enhancers	NHDF-Ad	bronchial
26	chr2:20069400-20069800	Enhancers	Primary B cells from peripheral blood	blood
27	chr2:20069400-20069800	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr2:20069400-20069800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:20069400-20069800	Weak transcription	Esophagus	oesophagus
30	chr2:20069400-20070000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:20069400-20070000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr2:20069400-20070000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr2:20069400-20070000	Enhancers	Fetal Intestine Large	intestine
34	chr2:20069400-20070000	Genic enhancers	Fetal Intestine Small	intestine
35	chr2:20069400-20070000	Enhancers	Fetal Muscle Trunk	muscle
36	chr2:20069400-20070400	Enhancers	Primary T cells fromperipheralblood	blood
37	chr2:20069400-20070800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr2:20069400-20070800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr2:20069400-20071200	Weak transcription	Fetal Stomach	stomach
40	chr2:20069400-20072800	Weak transcription	Primary B cells from cord blood	blood
41	chr2:20069400-20075600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:20069400-20075800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:20069400-20076000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:20069400-20076200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:20069400-20078600	Weak transcription	Placenta	Placenta

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