Variant report

Variant	rs12540497
Chromosome Location	chr7:104413849-104413850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:104412687..104414288-chr7:104414612..104417316,2	K562	blood:
2	chr7:104409406..104411368-chr7:104413418..104415967,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10270391	0.81[JPT][hapmap]
rs12540437	0.86[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12705276	0.85[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12705277	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12705278	0.82[JPT][hapmap]
rs13236549	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs13243476	0.82[JPT][hapmap]
rs13310494	0.89[ASW][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs34680468	0.84[ASN][1000 genomes]
rs34838562	0.92[ASN][1000 genomes]
rs4283980	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs4400324	0.85[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs57968847	0.93[ASN][1000 genomes]
rs61651012	0.97[ASN][1000 genomes]
rs6466019	0.84[YRI][hapmap]
rs6950832	0.96[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	nsv429790	chr7:104314049-104488049	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv429792	chr7:104400049-104488049	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5887	chr7:104401250-104491604	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1030875	chr7:104409391-104472647	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1028479	chr7:104409391-104479087	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv528392	chr7:104411273-104466675	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv522743	chr7:104411273-104486707	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12540497	ATXN7L1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104409400-104414200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:104411400-104414400	Enhancers	H1 Cell Line	embryonic stem cell
3	chr7:104412400-104414000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:104412600-104414200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr7:104412600-104414400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:104412600-104414600	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr7:104412800-104414200	Enhancers	Fetal Brain Female	brain
8	chr7:104412800-104414400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr7:104412800-104414800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:104412800-104415800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:104413000-104414200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:104413000-104414400	Enhancers	Brain Hippocampus Middle	brain
13	chr7:104413000-104414600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr7:104413200-104414600	Enhancers	Brain Anterior Caudate	brain
15	chr7:104413200-104417800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:104413400-104414400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr7:104413400-104414400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:104413400-104414800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr7:104413400-104416000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr7:104413800-104417000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr7:104413800-104424000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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