Variant report

Variant	rs11898449
Chromosome Location	chr2:20346809-20346810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20337444..20339646-chr2:20346771..20348752,3	K562	blood:
2	chr2:20342469..20346864-chr2:20382569..20386022,5	MCF-7	breast:
3	chr2:20343488..20346809-chr2:20347899..20350701,3	MCF-7	breast:
4	chr2:20344027..20347003-chr2:20348055..20350773,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs73227769	0.96[AFR][1000 genomes]
rs73227783	1.00[AFR][1000 genomes]
rs73229414	0.83[AFR][1000 genomes]

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	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1012055	chr2:20336237-20356606	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1005923	chr2:20344028-20369781	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv581156	chr2:20346312-20356944	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20332200-20364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:20339600-20349200	Weak transcription	Small Intestine	intestine
3	chr2:20339800-20348200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:20340000-20348000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:20340000-20348400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:20340200-20348400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:20340800-20347200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:20341800-20348600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:20341800-20348600	Weak transcription	Adipose Nuclei	Adipose
10	chr2:20341800-20348800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:20342000-20348000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:20342000-20348200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:20342000-20348400	Weak transcription	NHLF	lung
14	chr2:20342000-20348600	Weak transcription	Hela-S3	cervix
15	chr2:20342800-20347000	Enhancers	Stomach Mucosa	stomach
16	chr2:20343400-20348400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:20344000-20348200	Weak transcription	NH-A	brain
18	chr2:20345200-20348200	Weak transcription	HUVEC	blood vessel
19	chr2:20345600-20349800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:20345600-20356600	Weak transcription	Liver	Liver
21	chr2:20345800-20347800	Weak transcription	Lung	lung
22	chr2:20345800-20348000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:20345800-20348600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:20345800-20348600	Weak transcription	A549	lung
25	chr2:20345800-20349200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:20345800-20349200	Weak transcription	Gastric	stomach
27	chr2:20346000-20348000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:20346000-20348200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:20346000-20348400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:20346000-20348400	Weak transcription	HSMMtube	muscle
31	chr2:20346000-20348600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:20346000-20348800	Weak transcription	Fetal Intestine Large	intestine
33	chr2:20346000-20349400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:20346000-20355600	Weak transcription	Esophagus	oesophagus
35	chr2:20346200-20348200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:20346200-20348400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:20346200-20348600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:20346200-20348600	Weak transcription	Fetal Intestine Small	intestine
39	chr2:20346400-20348400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:20346400-20348400	Weak transcription	Fetal Lung	lung
41	chr2:20346400-20348400	Weak transcription	K562	blood
42	chr2:20346400-20349200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:20346600-20348600	Weak transcription	Placenta	Placenta
44	chr2:20346600-20348800	Weak transcription	NHEK	skin
45	chr2:20346800-20347000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:20346800-20347200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:20346800-20347800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:20346800-20347800	Weak transcription	Osteobl	bone
49	chr2:20346800-20348000	Weak transcription	NHDF-Ad	bronchial
50	chr2:20346800-20348200	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links