Variant report

Variant	rs6433688
Chromosome Location	chr2:178537676-178537677
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178128784..178131655-chr2:178537635..178541213,3	K562	blood:
2	chr2:178536377..178538004-chr2:178556463..178558808,2	K562	blood:
3	chr2:178128784..178131655-chr2:178537635..178540049,2	K562	blood:
4	chr2:178533626..178535228-chr2:178535564..178538374,2	K562	blood:
5	chr1:67678579..67680079-chr2:178536885..178539298,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116044	Chromatin interaction
ENSG00000222043	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10497497	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10803912	0.80[MEX][hapmap]
rs11679730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680632	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12468046	1.00[CHD][hapmap]
rs12618150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12620285	1.00[CHB][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13017234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13026012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317945	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431105	1.00[CHB][hapmap]
rs1358326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446839	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs1527400	0.84[GIH][hapmap]
rs1527403	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534305	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1544001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17326999	1.00[CHD][hapmap]
rs1918345	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918346	0.93[EUR][1000 genomes]
rs1918347	0.99[EUR][1000 genomes]
rs1997206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997207	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091442	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178017	1.00[CHD][hapmap];0.80[MEX][hapmap]
rs2222712	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365621	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695315	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap]
rs4110134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341975	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893829	0.80[MEX][hapmap]
rs4893970	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893973	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893975	0.84[GIH][hapmap]
rs4893978	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893979	0.95[EUR][1000 genomes]
rs5025340	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433672	1.00[CHD][hapmap];0.80[MEX][hapmap]
rs6433685	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433686	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433687	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721360	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723031	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6723063	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs6746233	0.83[EUR][1000 genomes]
rs6755382	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6756918	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7560080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560514	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573345	1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7577552	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7597640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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	nsv431812	chr2:178525371-178584470	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1007925	chr2:178535922-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6433688	AGPS	cis	cerebellum	SCAN
rs6433688	PRKRA	cis	parietal	SCAN
rs6433688	TTC30B	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178531400-178540000	Weak transcription	K562	blood
2	chr2:178532800-178538000	Weak transcription	HSMM	muscle
3	chr2:178535000-178544800	Weak transcription	Right Atrium	heart
4	chr2:178535400-178540000	Weak transcription	Liver	Liver
5	chr2:178536000-178540000	Weak transcription	Brain Substantia Nigra	brain
6	chr2:178536000-178540000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:178536000-178544600	Weak transcription	Psoas Muscle	Psoas
8	chr2:178536200-178540200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:178536200-178540200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:178536600-178540400	Weak transcription	Fetal Stomach	stomach
11	chr2:178536600-178556000	Weak transcription	Pancreas	Pancrea
12	chr2:178537000-178540000	Weak transcription	Fetal Kidney	kidney
13	chr2:178537000-178540200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:178537200-178539600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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