Variant report

Variant	rs2253711
Chromosome Location	chr7:69061698-69061699
allele	C/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	POLR2A	chr7:69061661-69062082	H1-neurons	neurons:	n/a	n/a
2	MXI1	chr7:69060600-69067258	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AUTS2-1	chr7:69061156-69063004	XLOC_006142

Variant related genes	Relation type
AUTS2	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10085775	0.82[AMR][1000 genomes]
rs1014382	0.85[AMR][1000 genomes]
rs10237145	0.84[AMR][1000 genomes]
rs10241485	0.83[AMR][1000 genomes]
rs10950191	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12333508	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12531914	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12669765	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1468588	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2058395	0.83[AMR][1000 genomes]
rs210598	0.83[AMR][1000 genomes]
rs210600	0.80[AMR][1000 genomes]
rs210603	0.85[AMR][1000 genomes]
rs2533432	0.85[AMR][1000 genomes]
rs2533434	0.85[AMR][1000 genomes]
rs2533440	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2533446	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2533447	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2533456	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2851485	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2851488	0.85[AMR][1000 genomes]
rs2851500	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2851504	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2851509	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2851512	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2851517	0.85[AMR][1000 genomes]
rs41851	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41855	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs41858	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4717521	0.83[AMR][1000 genomes]
rs563740	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs588004	0.85[AMR][1000 genomes]
rs608796	0.83[AMR][1000 genomes]
rs611052	0.85[AMR][1000 genomes]
rs611573	0.80[AMR][1000 genomes]
rs622767	0.83[AMR][1000 genomes]
rs624626	0.85[AMR][1000 genomes]
rs674865	0.85[AMR][1000 genomes]
rs6955815	0.81[AMR][1000 genomes]
rs6957302	0.82[AMR][1000 genomes]
rs6959766	0.83[AMR][1000 genomes]
rs6974004	0.83[AMR][1000 genomes]
rs720056	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs917616	0.85[AMR][1000 genomes]
rs9692258	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs981291	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs988282	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023885	chr7:68894896-69158290	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538915	chr7:68894896-69158290	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv428169	chr7:69021482-69196743	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv5783	chr7:69048608-69066760	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69057000-69061800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:69058400-69062000	Weak transcription	Fetal Intestine Small	intestine
3	chr7:69061000-69061800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr7:69061200-69061800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:69061200-69062000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:69061200-69062000	Enhancers	Primary hematopoietic stem cells	blood
7	chr7:69061400-69062000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr7:69061600-69061800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:69061600-69061800	Enhancers	Adipose Nuclei	Adipose
10	chr7:69061600-69061800	Bivalent Enhancer	Colonic Mucosa	Colon
11	chr7:69061600-69062000	Enhancers	Brain Cingulate Gyrus	brain
12	chr7:69061600-69062000	Enhancers	Colon Smooth Muscle	Colon
13	chr7:69061600-69062000	Enhancers	Dnd41	blood
14	chr7:69061600-69062200	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr7:69061600-69062400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:69061600-69065800	Active TSS	Brain Angular Gyrus	brain

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