Variant report

Variant	rs2253795
Chromosome Location	chr3:53778875-53778876
allele	A/C
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	MAX	chr3:53778358-53778877	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:53778754-53778880	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53777857..53780018-chr3:53784994..53786883,2	K562	blood:

Variant related genes	Relation type
CACNA1D	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11705918	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs11720848	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2612012	0.87[CEU][hapmap]
rs2612028	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680648	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35146621	0.85[AMR][1000 genomes]
rs35447065	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3774573	0.95[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs3774574	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3774583	0.90[CEU][hapmap];0.89[CHB][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3774595	0.84[CEU][hapmap]
rs719260	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.87[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73092085	0.88[EUR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1002452	chr3:53742148-53802811	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv520027	chr3:53762713-53784625	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2253795	ACTR8	cis	parietal	SCAN
rs2253795	IL17RB	cis	cerebellum	SCAN
rs2253795	HEMK1	cis	cerebellum	SCAN
rs2253795	SEMA3G	cis	parietal	SCAN
rs2253795	NPRL2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53761600-53781800	Weak transcription	Spleen	Spleen
2	chr3:53764200-53779800	Weak transcription	Liver	Liver
3	chr3:53764800-53783400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:53765000-53779800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:53765000-53779800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:53765000-53788600	Weak transcription	Fetal Kidney	kidney
7	chr3:53765200-53783400	Weak transcription	Brain Angular Gyrus	brain
8	chr3:53765400-53781600	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:53766600-53781200	Weak transcription	Lung	lung
10	chr3:53768600-53801000	Strong transcription	Fetal Lung	lung
11	chr3:53769600-53787400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:53770200-53779800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:53773000-53807600	Strong transcription	Fetal Intestine Large	intestine
14	chr3:53774200-53789200	Weak transcription	Fetal Brain Male	brain
15	chr3:53774400-53782000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:53774600-53785000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:53774800-53807200	Strong transcription	Fetal Intestine Small	intestine
18	chr3:53775800-53779400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:53777800-53779000	Enhancers	Fetal Thymus	thymus
20	chr3:53777800-53787600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:53778000-53779800	Enhancers	GM12878-XiMat	blood
22	chr3:53778400-53779000	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr3:53778400-53779000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr3:53778400-53781400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:53778400-53781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:53778600-53806400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:53778800-53781600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:53778800-53781800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:53778800-53781800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:53778800-53783800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:53778800-53797000	Weak transcription	Pancreas	Pancrea

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