Variant report

Variant	rs7572263
Chromosome Location	chr2:209051586-209051587
allele	A/G
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	SP1	chr2:209051569-209052019	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr2:209051547-209052022	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:209049851..209051700-chr2:209064881..209067497,2	K562	blood:

Variant related genes	Relation type
C2orf80	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10192397	0.82[JPT][hapmap]
rs10497896	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10804167	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11676550	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11883992	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12373582	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap]
rs12986551	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12995124	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12995271	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1992739	1.00[CHB][hapmap]
rs34029379	1.00[ASN][1000 genomes]
rs34082227	1.00[ASN][1000 genomes]
rs34575089	0.81[ASN][1000 genomes]
rs35551278	1.00[ASN][1000 genomes]
rs6704765	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6705133	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6710217	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710543	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6719638	1.00[CHB][hapmap]
rs6725512	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749281	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6751157	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6751646	1.00[JPT][hapmap]
rs67989853	1.00[ASN][1000 genomes]
rs71418664	1.00[ASN][1000 genomes]
rs71418665	1.00[ASN][1000 genomes]
rs72974837	0.93[ASN][1000 genomes]
rs7579275	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7579623	1.00[ASN][1000 genomes]
rs7583625	0.95[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9646836	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv584298	chr2:209021232-209052303	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv584299	chr2:209021232-209067051	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv875749	chr2:209022909-209062388	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv875750	chr2:209022909-209069303	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv869592	chr2:209029861-209060862	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv584300	chr2:209033557-209054928	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv2763083	chr2:209033581-209058397	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv584301	chr2:209034715-209054928	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv875751	chr2:209042963-209110784	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7572263	FASTKD2	cis	parietal	SCAN
rs7572263	RPE	cis	parietal	SCAN
rs7572263	IDH1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209040000-209064000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:209049200-209051600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:209049200-209051800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:209049400-209051800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:209049400-209052000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr2:209049400-209052800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr2:209049600-209052000	Weak transcription	Liver	Liver
8	chr2:209049800-209051600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:209049800-209052000	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr2:209049800-209053400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:209050000-209051800	Active TSS	Brain Anterior Caudate	brain
12	chr2:209050200-209051600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:209050200-209053600	Weak transcription	Brain Germinal Matrix	brain
14	chr2:209050800-209052000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:209051200-209051600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:209051200-209051800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:209051200-209051800	Active TSS	Brain Angular Gyrus	brain
18	chr2:209051200-209052000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr2:209051200-209052000	Enhancers	Fetal Brain Male	brain
20	chr2:209051200-209052000	Enhancers	Fetal Thymus	thymus
21	chr2:209051200-209055200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:209051400-209051600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr2:209051400-209051600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:209051400-209051800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:209051400-209051800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
26	chr2:209051400-209051800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
27	chr2:209051400-209052200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:209051400-209052400	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr2:209051400-209052800	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links