Variant report

Variant	rs9879081
Chromosome Location	chr3:143706302-143706303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:79202497..79203306-chr3:143705462..143706390,2	MCF-7	breast:
2	chr3:143705634..143708204-chr3:143731151..143734050,2	K562	blood:
3	chr3:143689459..143694662-chr3:143702114..143706390,7	K562	blood:
4	chr3:143689026..143691160-chr3:143705975..143707584,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10513239	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs11720435	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11917772	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13317365	0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13320111	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1604886	0.81[EUR][1000 genomes]
rs2370173	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28627639	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56880774	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6776760	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73000690	0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73002695	0.96[EUR][1000 genomes]
rs73002698	0.96[EUR][1000 genomes]
rs73872672	0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7627966	0.96[EUR][1000 genomes]
rs7637012	0.81[EUR][1000 genomes]
rs964572	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9823162	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9834740	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9835993	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847681	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9849618	0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9860540	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9861563	0.98[EUR][1000 genomes]
rs9866992	0.85[AMR][1000 genomes]
rs9870939	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9874033	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876107	0.97[AMR][1000 genomes];0.88[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	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143692600-143707800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:143692800-143714200	Weak transcription	Small Intestine	intestine
3	chr3:143693400-143706800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:143693400-143708400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:143693400-143708400	Weak transcription	Psoas Muscle	Psoas
6	chr3:143693400-143713800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:143693600-143711600	Weak transcription	Left Ventricle	heart
8	chr3:143694000-143708000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:143694400-143708400	Weak transcription	Fetal Intestine Small	intestine
10	chr3:143694400-143718800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:143694400-143719400	Weak transcription	Hela-S3	cervix
12	chr3:143694800-143707200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:143695600-143710200	Weak transcription	Fetal Brain Male	brain
14	chr3:143695600-143716800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:143696400-143711600	Weak transcription	Fetal Brain Female	brain
16	chr3:143696400-143711800	Weak transcription	Fetal Intestine Large	intestine
17	chr3:143696800-143706600	Weak transcription	Ovary	ovary
18	chr3:143697000-143708000	Weak transcription	HUVEC	blood vessel
19	chr3:143697000-143708400	Weak transcription	K562	blood
20	chr3:143697000-143713400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:143697000-143722800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:143697000-143729200	Weak transcription	Aorta	Aorta
23	chr3:143697200-143708400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:143697200-143708400	Weak transcription	HMEC	breast
25	chr3:143697200-143708400	Weak transcription	NHEK	skin
26	chr3:143697200-143710200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr3:143697200-143712000	Weak transcription	Adipose Nuclei	Adipose
28	chr3:143697200-143723000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:143697200-143727800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:143697400-143708400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:143697800-143707800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:143697800-143707800	Weak transcription	Dnd41	blood
33	chr3:143697800-143708000	Weak transcription	Liver	Liver
34	chr3:143698000-143711000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:143698200-143708400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:143698400-143708400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:143698400-143708400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:143698400-143721200	Weak transcription	Fetal Kidney	kidney
39	chr3:143698600-143707800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:143698800-143708400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:143699000-143707800	Weak transcription	Fetal Lung	lung
42	chr3:143699000-143708400	Weak transcription	NHLF	lung
43	chr3:143699000-143717000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:143699200-143737600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:143699400-143706400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:143699400-143712200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:143699400-143714000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:143700400-143708400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:143700400-143720400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:143700600-143708400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links