Variant report

Variant	rs7340510
Chromosome Location	chr2:134267369-134267370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:134265911..134268884-chr2:134269496..134274997,4	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10165238	0.82[CEU][hapmap]
rs1016837	0.85[AMR][1000 genomes]
rs1017366	1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs10206425	1.00[CEU][hapmap]
rs11891880	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11903204	0.81[EUR][1000 genomes]
rs13399787	1.00[CEU][hapmap]
rs13408209	1.00[CEU][hapmap]
rs16825505	1.00[CEU][hapmap]
rs16825509	1.00[CEU][hapmap]
rs16826050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16826052	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16826544	1.00[JPT][hapmap]
rs17815418	1.00[CEU][hapmap]
rs60316439	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61578634	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720995	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6730679	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6732077	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990470	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72990471	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72990476	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990483	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990486	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990490	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990493	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990494	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72992306	0.81[EUR][1000 genomes]
rs72992325	0.81[EUR][1000 genomes]
rs72992334	0.81[EUR][1000 genomes]
rs72992339	0.81[EUR][1000 genomes]
rs72992347	0.81[EUR][1000 genomes]
rs72992351	0.81[EUR][1000 genomes]
rs72992377	0.81[EUR][1000 genomes]
rs73003136	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73003138	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003141	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003144	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003146	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7340446	0.82[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9917399	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.97[LWK][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2830192	chr2:134259612-134311713	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7340510	HP	trans	brain	seeQTL
rs7340510	PRELP	trans	brain	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134262000-134267600	Enhancers	Brain Germinal Matrix	brain
2	chr2:134262600-134267400	Weak transcription	Esophagus	oesophagus
3	chr2:134263200-134268600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:134264200-134268200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:134264400-134267600	Enhancers	Brain Substantia Nigra	brain
6	chr2:134264800-134267600	Enhancers	Brain Hippocampus Middle	brain
7	chr2:134265200-134267400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:134265600-134267400	Enhancers	Fetal Brain Male	brain
9	chr2:134265600-134267800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:134266800-134267400	Enhancers	Brain Cingulate Gyrus	brain
11	chr2:134266800-134267600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:134266800-134268000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:134266800-134270600	Weak transcription	Brain Anterior Caudate	brain
14	chr2:134266800-134271000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:134266800-134273000	Weak transcription	Brain Angular Gyrus	brain
16	chr2:134266800-134273800	Weak transcription	Fetal Brain Female	brain
17	chr2:134267000-134267800	Enhancers	HMEC	breast
18	chr2:134267000-134267800	Enhancers	NHEK	skin
19	chr2:134267000-134275200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:134267200-134268000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:134267200-134268200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links