Variant report

Variant	rs3731198
Chromosome Location	chr9:21989477-21989478
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:21811532..21820564-chr9:21988281..21997291,17	MCF-7	breast:
2	chr9:21811237..21820561-chr9:21988636..21997115,18	MCF-7	breast:
3	chr9:21989242..21991114-chr9:22008985..22011051,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDKN2B-2	chr9:21989339-21989954	NONHSAT130411

Variant related genes	Relation type
ENSG00000229298	Chromatin interaction
ENSG00000147883	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10738604	1.00[YRI][hapmap]
rs13297747	0.83[EUR][1000 genomes]
rs13298881	1.00[YRI][hapmap]
rs2188127	0.81[EUR][1000 genomes]
rs2518719	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2811711	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3731204	1.00[CEU][hapmap]
rs3731217	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3731222	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs495490	0.86[CEU][hapmap]
rs545226	1.00[YRI][hapmap]
rs575427	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1821117	chr9:21933029-22012229	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1018514	chr9:21944275-22075326	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv892746	chr9:21953137-22028801	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv3492902	chr9:21971026-22006145	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv3492901	chr9:21971095-22006263	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv892747	chr9:21984661-22068646	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21987200-21992800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:21988000-21989600	Weak transcription	HSMM	muscle
3	chr9:21988000-21993000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr9:21988200-21990000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:21988400-21990800	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr9:21988800-21989600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:21989000-21989600	Weak transcription	HMEC	breast
8	chr9:21989000-21989600	Enhancers	NHEK	skin
9	chr9:21989000-21990200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:21989200-21989600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:21989200-21989600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:21989200-21989600	Enhancers	NH-A	brain
13	chr9:21989400-21989600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
14	chr9:21989400-21989600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr9:21989400-21989600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:21989400-21989600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr9:21989400-21989600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
18	chr9:21989400-21989600	Active TSS	Osteobl	bone
19	chr9:21989400-21989800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
20	chr9:21989400-21990000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
21	chr9:21989400-21990400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:21989400-21990400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:21989400-21990400	Flanking Active TSS	NHLF	lung
24	chr9:21989400-21990600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:21989400-21990600	Flanking Active TSS	NHDF-Ad	bronchial
26	chr9:21989400-21990800	ZNF genes & repeats	GM12878-XiMat	blood
27	chr9:21989400-21991000	Transcr. at gene 5' and 3'	Hela-S3	cervix
28	chr9:21989400-21991200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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