Variant report

Variant	rs7587317
Chromosome Location	chr2:10234179-10234180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:10234120-10234270	WERI-Rb-1	eye:	n/a	n/a
2	RFX5	chr2:10234027-10234936	SK-N-SH	brain:	n/a	chr2:10234560-10234575 chr2:10234558-10234572 chr2:10234561-10234570 chr2:10234559-10234576 chr2:10234562-10234577 chr2:10234560-10234575 chr2:10234560-10234575

No.	Distal block	Cell Line	Cell type
1	chr2:10228308..10230479-chr2:10232998..10234786,2	MCF-7	breast:
2	chr2:10234144..10239226-chr2:10260228..10264848,7	K562	blood:
3	chr2:10228504..10230322-chr2:10232786..10235690,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212558	TF binding region
ENSG00000171848	Chromatin interaction
ENSG00000212558	Chromatin interaction
ENSG00000272524	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10177872	1.00[ASN][1000 genomes]
rs10929632	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1138729	1.00[CHB][hapmap]
rs11886661	1.00[ASN][1000 genomes]
rs12992149	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13400128	1.00[ASN][1000 genomes]
rs3935840	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302193	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321336	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485541	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569449	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669528	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4669536	1.00[CHB][hapmap]
rs4669545	1.00[CHB][hapmap]
rs6432058	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432060	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432063	1.00[CHB][hapmap]
rs6706848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs72786623	1.00[ASN][1000 genomes]
rs72786624	1.00[ASN][1000 genomes]
rs7574663	1.00[CHB][hapmap]
rs7582263	1.00[CHB][hapmap]
rs7585544	1.00[CHB][hapmap]
rs7587529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602408	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];1.00[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	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1007965	chr2:10154960-10276125	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1014790	chr2:10156968-10274855	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv999019	chr2:10157762-10273232	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
7	nsv873633	chr2:10175442-10266563	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv1010706	chr2:10189219-10266995	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7587317	CYS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10231400-10236600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:10232000-10236800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:10232000-10236800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:10232000-10240200	Weak transcription	Right Atrium	heart
5	chr2:10232000-10242600	Weak transcription	Pancreas	Pancrea
6	chr2:10233000-10234400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:10233800-10234800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:10234000-10235000	Enhancers	Brain Germinal Matrix	brain
9	chr2:10234000-10235200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr2:10234000-10235800	Enhancers	Fetal Brain Male	brain
11	chr2:10234000-10237600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:10234000-10237600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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