Variant report

Variant	rs6723063
Chromosome Location	chr2:178491398-178491399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178490562..178493751-chr2:178498705..178503907,5	K562	blood:
2	chr2:178489030..178493776-chr2:178494411..178499893,10	K562	blood:
3	chr2:178482511..178485176-chr2:178490734..178492926,2	K562	blood:

Variant related genes	Relation type
ENSG00000197557	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10181259	0.84[CEU][hapmap]
rs10201367	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10201883	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10497497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497499	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10497504	0.84[CEU][hapmap]
rs10803912	0.84[CEU][hapmap]
rs11679519	0.83[CEU][hapmap]
rs11679730	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs11680632	1.00[CHB][hapmap]
rs11694013	0.89[EUR][1000 genomes]
rs11694988	0.91[CEU][hapmap]
rs11889272	0.84[CEU][hapmap]
rs12468046	1.00[CHD][hapmap]
rs12618150	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs12620285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621156	1.00[CHD][hapmap]
rs12988366	0.91[CEU][hapmap];0.88[MEX][hapmap]
rs13014417	0.84[CEU][hapmap]
rs13017234	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs13017429	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs13025391	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs13025904	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs13026012	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs13028757	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs1317945	0.86[ASN][1000 genomes]
rs13431091	0.84[CEU][hapmap]
rs13431105	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs1345138	0.84[CEU][hapmap]
rs1348851	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs1358326	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs1358327	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1374438	0.84[CEU][hapmap]
rs1446839	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1527403	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1534305	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544001	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17326999	1.00[CHD][hapmap]
rs1852530	0.91[CEU][hapmap]
rs1867905	0.84[CEU][hapmap]
rs1918345	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1997206	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1997207	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2091442	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2178017	0.84[CEU][hapmap];1.00[CHD][hapmap]
rs2218575	0.84[CEU][hapmap]
rs2222712	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2293475	0.84[CEU][hapmap]
rs2365620	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2365621	0.86[ASN][1000 genomes]
rs2695315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs4110134	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4144278	0.84[CEU][hapmap]
rs4243389	0.84[CEU][hapmap]
rs4341975	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4893827	1.00[CHD][hapmap]
rs4893829	0.84[CEU][hapmap]
rs4893956	0.84[CEU][hapmap]
rs4893967	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4893970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893973	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893978	0.86[ASN][1000 genomes]
rs5025340	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57986285	0.83[EUR][1000 genomes]
rs58160847	0.84[EUR][1000 genomes]
rs6433672	0.84[CEU][hapmap];1.00[CHD][hapmap]
rs6433685	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6433686	0.86[ASN][1000 genomes]
rs6433687	0.86[ASN][1000 genomes]
rs6433688	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs6710109	0.84[CEU][hapmap]
rs6720483	1.00[CHD][hapmap]
rs6721360	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6723014	0.84[CEU][hapmap]
rs6723031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746233	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6756918	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560080	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7560514	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7560737	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs7573345	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs7577552	0.86[ASN][1000 genomes]
rs7578901	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7582179	0.91[CEU][hapmap]
rs7586934	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs7588049	0.84[CEU][hapmap]
rs7593744	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7593753	1.00[CHB][hapmap]
rs7597640	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs935426	0.84[CEU][hapmap]
rs941271	1.00[CHB][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv583689	chr2:178468008-178509820	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6723063	PRKRA	cis	parietal	SCAN
rs6723063	TTC30B	cis	parietal	SCAN
rs6723063	OSBPL6	cis	parietal	SCAN
rs6723063	AGPS	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178484000-178499200	Weak transcription	Pancreas	Pancrea
2	chr2:178488000-178498800	Weak transcription	Fetal Kidney	kidney
3	chr2:178488400-178493400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:178490200-178491800	Enhancers	Fetal Brain Male	brain
5	chr2:178490600-178491400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:178490600-178491400	Enhancers	Brain Cingulate Gyrus	brain
7	chr2:178490600-178491400	Active TSS	Duodenum Mucosa	Duodenum
8	chr2:178490600-178491400	Flanking Active TSS	K562	blood
9	chr2:178490600-178491600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr2:178490600-178491600	Enhancers	Fetal Thymus	thymus
11	chr2:178490800-178491400	Flanking Active TSS	Fetal Brain Female	brain
12	chr2:178490800-178491400	Flanking Active TSS	GM12878-XiMat	blood
13	chr2:178490800-178491600	Active TSS	Brain Anterior Caudate	brain
14	chr2:178490800-178491600	Enhancers	Brain Substantia Nigra	brain
15	chr2:178490800-178491600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr2:178490800-178491600	Enhancers	Placenta	Placenta
17	chr2:178491000-178491400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr2:178491000-178491400	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr2:178491000-178491400	Enhancers	Brain Germinal Matrix	brain
20	chr2:178491000-178491400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:178491000-178491600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr2:178491000-178493800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:178491000-178494600	Weak transcription	HepG2	liver
24	chr2:178491200-178491400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr2:178491200-178491400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:178491200-178491600	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr2:178491200-178491600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr2:178491200-178493600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:178491200-178493800	Weak transcription	Brain Angular Gyrus	brain
30	chr2:178491200-178493800	Weak transcription	Brain Inferior Temporal Lobe	brain

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