Variant report

Variant	rs2280142
Chromosome Location	chr2:99434872-99434873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99434258..99436227-chr2:99437551..99439851,2	MCF-7	breast:
2	chr2:99430065..99431888-chr2:99433157..99434960,2	MCF-7	breast:
3	chr2:99434724..99436246-chr2:99444476..99446332,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10174531	0.90[ASN][1000 genomes]
rs10175560	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10182043	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10202643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123754	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11900176	0.82[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11900524	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12712034	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12712037	0.82[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12990579	0.82[CEU][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13005148	0.81[EUR][1000 genomes]
rs2276604	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs6542837	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542839	0.81[MEX][hapmap]
rs6714330	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739097	0.82[EUR][1000 genomes]
rs6753465	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6753879	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6755640	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6757098	0.85[MEX][hapmap]
rs6760065	0.85[MEX][hapmap]
rs73962464	0.89[ASN][1000 genomes]
rs7423519	0.85[MEX][hapmap]
rs7560696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7565614	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7565736	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7590596	0.81[EUR][1000 genomes]
rs885115	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2280142	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99418000-99442200	Weak transcription	Stomach Mucosa	stomach
2	chr2:99423400-99439200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:99423600-99439200	Weak transcription	Brain Angular Gyrus	brain
4	chr2:99424000-99435600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:99424000-99438400	Weak transcription	Pancreas	Pancrea
6	chr2:99426800-99439200	Weak transcription	Gastric	stomach
7	chr2:99427200-99439000	Weak transcription	Aorta	Aorta
8	chr2:99427400-99442000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:99427600-99437200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:99427600-99438000	Weak transcription	Fetal Intestine Large	intestine
11	chr2:99432600-99435200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:99432600-99436400	Weak transcription	Fetal Intestine Small	intestine
13	chr2:99432600-99437000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:99433400-99438200	Weak transcription	Colonic Mucosa	Colon
15	chr2:99434000-99435400	Enhancers	Lung	lung
16	chr2:99434200-99436200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr2:99434400-99435400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:99434600-99435200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:99434600-99435200	Enhancers	HUVEC	blood vessel
20	chr2:99434600-99435400	Enhancers	HMEC	breast
21	chr2:99434600-99435800	Enhancers	Left Ventricle	heart
22	chr2:99434600-99436000	Enhancers	Right Atrium	heart
23	chr2:99434600-99436200	Enhancers	Brain Anterior Caudate	brain
24	chr2:99434600-99438200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr2:99434800-99435200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:99434800-99435200	Weak transcription	Esophagus	oesophagus
27	chr2:99434800-99435200	Enhancers	Fetal Lung	lung
28	chr2:99434800-99435200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr2:99434800-99435800	Weak transcription	Right Ventricle	heart
30	chr2:99434800-99436400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:99434800-99436400	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links