Variant report

Variant	rs10173499
Chromosome Location	chr2:100877652-100877653
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:100877002..100888885-chr2:100934823..100940762,23	MCF-7	breast:
2	chr2:100876921..100878044-chr2:100997529..100998340,3	K562	blood:
3	chr2:100684789..100685779-chr2:100877301..100878058,2	MCF-7	breast:
4	chr2:100873599..100875237-chr2:100876970..100878624,2	MCF-7	breast:
5	chr2:100059471..100059973-chr2:100877276..100877813,2	K562	blood:
6	chr2:100876984..100878779-chr2:101034439..101036226,2	K562	blood:
7	chr2:100876613..100880348-chr2:101031611..101035939,8	K562	blood:
8	chr2:100175238..100176204-chr2:100876861..100877763,3	MCF-7	breast:
9	chr2:100875966..100878799-chr2:100906876..100908974,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115526	Chromatin interaction
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10170878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199107	0.81[EUR][1000 genomes]
rs10865039	1.00[JPT][hapmap]
rs11886523	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12463633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464505	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12467008	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12472141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12611915	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13394110	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13397010	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13397337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309815	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs2309817	1.00[JPT][hapmap]
rs2309822	1.00[JPT][hapmap]
rs2309823	1.00[JPT][hapmap]
rs2309824	1.00[JPT][hapmap]
rs2871341	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34044131	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851281	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851282	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851287	1.00[JPT][hapmap]
rs55856206	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57328601	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60501704	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62148117	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62148118	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6542919	1.00[JPT][hapmap]
rs6542923	1.00[JPT][hapmap]
rs6542924	1.00[JPT][hapmap]
rs6707358	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724490	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72819202	0.84[AMR][1000 genomes]
rs72821104	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72821119	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72821120	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72821122	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72821124	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72821125	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72821126	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72821130	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72821133	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559464	1.00[JPT][hapmap]
rs7562372	1.00[JPT][hapmap]
rs7582180	1.00[JPT][hapmap]
rs7588623	1.00[JPT][hapmap]

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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10173499	LONRF2	cis	parietal	SCAN
rs10173499	SLC9A2	cis	cerebellum	SCAN
rs10173499	CHST10	cis	parietal	SCAN
rs10173499	MEOX2	trans	cerebellum	SCAN
rs10173499	LMAN2L	cis	cerebellum	SCAN
rs10173499	LONRF2	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100864200-100879800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:100865800-100879800	Weak transcription	Right Atrium	heart
3	chr2:100874600-100879200	Weak transcription	Brain Angular Gyrus	brain
4	chr2:100874600-100891400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:100875200-100881600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:100877000-100877800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:100877000-100879200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:100877000-100879400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr2:100877200-100877800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:100877200-100877800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr2:100877200-100879200	Weak transcription	Fetal Lung	lung
12	chr2:100877400-100878000	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr2:100877400-100879200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:100877600-100877800	Enhancers	Placenta	Placenta
15	chr2:100877600-100879200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:100877600-100879200	Weak transcription	Brain Substantia Nigra	brain
17	chr2:100877600-100879800	Weak transcription	Fetal Brain Male	brain
18	chr2:100877600-100888600	Weak transcription	Ovary	ovary

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