Variant report

Variant	rs2240355
Chromosome Location	chr7:38783751-38783752
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38779167..38781371-chr7:38782858..38784712,2	MCF-7	breast:
2	chr7:38776633..38779094-chr7:38783053..38785057,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10232480	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11978728	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12532461	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs12538785	0.99[ASN][1000 genomes]
rs12701660	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13244313	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1473137	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs1978170	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2074656	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2240350	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286083	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286085	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286086	0.82[CHB][hapmap]
rs2286090	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286092	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286100	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286102	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392595	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2893567	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs3207255	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3779126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3801135	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs3801142	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3801144	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4430003	0.86[CHB][hapmap]
rs4720298	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720299	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723783	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723793	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs6462858	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6462859	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6462861	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6462862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6961672	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7785056	0.81[ASN][1000 genomes]
rs7785161	0.86[CHB][hapmap]
rs7788664	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs7794371	0.81[ASN][1000 genomes]
rs7803397	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs7811599	0.81[ASN][1000 genomes]
rs886646	0.84[CHB][hapmap]
rs9638944	0.86[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887965	chr7:38706384-38793243	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2240355	TBX20	cis	parietal	SCAN
rs2240355	DPY19L1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38749000-38803600	Weak transcription	Fetal Brain Male	brain
2	chr7:38755000-38791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:38757000-38784200	Weak transcription	HMEC	breast
4	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
5	chr7:38759200-38810200	Weak transcription	A549	lung
6	chr7:38759400-38810600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:38759600-38784200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:38760000-38799800	Weak transcription	HUVEC	blood vessel
9	chr7:38760600-38800200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr7:38761000-38820400	Weak transcription	Stomach Mucosa	stomach
11	chr7:38761200-38785400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:38762600-38793200	Weak transcription	Hela-S3	cervix
13	chr7:38763200-38828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr7:38763400-38792600	Weak transcription	Small Intestine	intestine
15	chr7:38763400-38828800	Weak transcription	HepG2	liver
16	chr7:38763800-38791600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr7:38764400-38787600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:38764800-38784200	Weak transcription	NHEK	skin
19	chr7:38765400-38784200	Weak transcription	NHLF	lung
20	chr7:38765400-38789600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:38765400-38802800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr7:38765600-38784200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr7:38765600-38784400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:38766000-38784200	Weak transcription	NH-A	brain
25	chr7:38766000-38791800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr7:38766600-38791600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr7:38766800-38784200	Weak transcription	NHDF-Ad	bronchial
28	chr7:38767200-38792600	Weak transcription	Colonic Mucosa	Colon
29	chr7:38767200-38802800	Weak transcription	Right Ventricle	heart
30	chr7:38767200-38805800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:38768400-38791200	Weak transcription	Brain Germinal Matrix	brain
32	chr7:38768400-38791800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr7:38768600-38784600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr7:38768600-38786000	Weak transcription	Esophagus	oesophagus
35	chr7:38768600-38786200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:38769800-38795000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr7:38771400-38784000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr7:38771800-38784400	Weak transcription	Fetal Lung	lung
39	chr7:38771800-38786400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:38774800-38787000	Strong transcription	Liver	Liver
41	chr7:38774800-38816800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:38775000-38787400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr7:38775000-38788400	Strong transcription	Primary T cells from cord blood	blood
44	chr7:38775200-38787000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:38775600-38791200	Weak transcription	HSMMtube	muscle
46	chr7:38775800-38786800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr7:38775800-38787000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:38775800-38816600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr7:38776000-38787600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr7:38776400-38792200	Weak transcription	Fetal Heart	heart

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