Variant report

Variant	rs2862743
Chromosome Location	chr3:142112572-142112573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142101830..142104324-chr3:142111923..142114107,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10935461	0.86[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11925693	0.88[CEU][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12695761	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061823	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075471	0.86[EUR][1000 genomes]
rs1825522	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2086933	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2171035	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2227928	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs2862744	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2862745	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2862746	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28708455	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816805	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3922730	0.91[CHB][hapmap]
rs4434160	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4441672	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4597728	0.80[ASN][1000 genomes]
rs4608715	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57177110	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440077	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440078	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440083	0.87[CHB][hapmap]
rs6440089	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs6769786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6772400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6775718	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6777255	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6780250	0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6782400	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs6782897	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792259	0.91[CHB][hapmap]
rs6799752	0.91[CHB][hapmap]
rs6800695	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6802631	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610557	0.91[CHB][hapmap]
rs7613664	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7627694	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641330	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap]
rs7646701	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7651071	0.95[CHB][hapmap]
rs7652687	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9289647	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289648	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9816736	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9820770	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9821271	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9826786	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828178	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9846960	0.80[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap]
rs9847364	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9855140	0.80[ASN][1000 genomes]
rs9861997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9869842	0.91[CHB][hapmap];0.95[CHD][hapmap]
rs9871402	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2757892	chr3:141728870-142129836	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2759182	chr3:141728870-142129836	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv522549	chr3:141812759-142164735	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1000083	chr3:141956718-142172666	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv877557	chr3:142090402-142150204	Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2862743	XRN1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142066800-142115000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:142072400-142114600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:142074000-142113800	Weak transcription	HMEC	breast
4	chr3:142076000-142136400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:142076800-142120200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:142076800-142138200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:142080000-142114000	Weak transcription	NHLF	lung
8	chr3:142083200-142113800	Weak transcription	Small Intestine	intestine
9	chr3:142083200-142114200	Weak transcription	A549	lung
10	chr3:142083400-142114800	Weak transcription	HepG2	liver
11	chr3:142083600-142158600	Weak transcription	NHEK	skin
12	chr3:142094000-142114000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:142096600-142113800	Weak transcription	HUVEC	blood vessel
14	chr3:142097000-142112600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:142099800-142112600	Weak transcription	Pancreas	Pancrea
16	chr3:142104400-142113000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:142105000-142151800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:142105600-142116600	Strong transcription	Adipose Nuclei	Adipose
19	chr3:142105600-142123000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:142105800-142112800	Weak transcription	NH-A	brain
21	chr3:142105800-142136600	Strong transcription	Fetal Intestine Large	intestine
22	chr3:142106600-142113200	Weak transcription	Hela-S3	cervix
23	chr3:142106800-142113800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:142106800-142114000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:142106800-142123000	Weak transcription	Fetal Brain Male	brain
26	chr3:142106800-142150800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:142107000-142112600	Weak transcription	Esophagus	oesophagus
28	chr3:142108000-142114000	Weak transcription	Gastric	stomach
29	chr3:142109000-142114000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:142109000-142114000	Weak transcription	Spleen	Spleen
31	chr3:142109200-142112600	Weak transcription	Fetal Intestine Small	intestine
32	chr3:142109200-142113000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:142109200-142114000	Weak transcription	Lung	lung
34	chr3:142109200-142117000	Weak transcription	Fetal Stomach	stomach
35	chr3:142109200-142141800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:142109400-142112800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:142109400-142113400	Weak transcription	Brain Angular Gyrus	brain
38	chr3:142109400-142113800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr3:142109400-142114000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:142109600-142113000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:142109600-142113000	Weak transcription	HSMM	muscle
42	chr3:142109600-142113800	Weak transcription	Brain Substantia Nigra	brain
43	chr3:142109600-142114000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:142109800-142112600	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:142109800-142112600	Weak transcription	K562	blood
46	chr3:142109800-142112800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:142109800-142113000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:142109800-142113000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr3:142109800-142114000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:142110000-142113800	Weak transcription	Fetal Heart	heart

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