Variant report

Variant	rs238249
Chromosome Location	chr1:45555836-45555837
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45478626..45481172-chr1:45552881..45556060,3	K562	blood:
2	chr1:45285124..45286764-chr1:45554135..45555887,2	K562	blood:
3	chr1:45285124..45287446-chr1:45552897..45556279,3	K562	blood:
4	chr1:45185912..45188809-chr1:45555640..45557709,2	K562	blood:

Variant related genes	Relation type
ENSG00000199377	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10789454	0.90[EUR][1000 genomes]
rs11211074	0.96[CEU][hapmap];0.88[CHB][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1144868	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11806438	1.00[ASN][1000 genomes]
rs11810239	0.98[ASN][1000 genomes]
rs1226670	1.00[ASN][1000 genomes]
rs1226733	0.98[ASN][1000 genomes]
rs1226734	0.98[ASN][1000 genomes]
rs1226735	0.83[ASN][1000 genomes]
rs1226746	1.00[ASN][1000 genomes]
rs1226747	0.88[CHB][hapmap];1.00[ASN][1000 genomes]
rs1226748	1.00[ASN][1000 genomes]
rs1226836	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1226914	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13374935	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs1612575	1.00[CHD][hapmap]
rs1782459	0.97[ASN][1000 genomes]
rs1938300	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1938301	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1938303	1.00[ASN][1000 genomes]
rs1938304	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1938407	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2088956	0.98[ASN][1000 genomes]
rs2105458	0.95[CEU][hapmap];0.88[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186219	0.96[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2202152	0.91[CHD][hapmap]
rs2228084	0.91[CHD][hapmap]
rs2356302	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2997458	0.83[EUR][1000 genomes]
rs2997461	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2997465	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3009968	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3009969	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3009974	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3009979	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121732	0.96[CEU][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3121769	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34134455	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs346684	0.82[CHB][hapmap];1.00[ASN][1000 genomes]
rs346687	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346693	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs346695	1.00[ASN][1000 genomes]
rs346696	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346697	1.00[ASN][1000 genomes]
rs346698	1.00[ASN][1000 genomes]
rs346700	1.00[ASN][1000 genomes]
rs346701	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346702	1.00[ASN][1000 genomes]
rs346703	1.00[CHD][hapmap]
rs346705	1.00[ASN][1000 genomes]
rs346706	0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[ASN][1000 genomes]
rs346707	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs346708	0.92[ASN][1000 genomes]
rs346712	1.00[ASN][1000 genomes]
rs346716	1.00[ASN][1000 genomes]
rs346717	0.88[CHB][hapmap];1.00[ASN][1000 genomes]
rs346719	0.88[CHB][hapmap];1.00[ASN][1000 genomes]
rs346721	1.00[ASN][1000 genomes]
rs346723	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346724	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs346725	1.00[CHD][hapmap]
rs346729	1.00[ASN][1000 genomes]
rs346731	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346732	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs346733	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346734	1.00[ASN][1000 genomes]
rs346735	1.00[ASN][1000 genomes]
rs346736	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346737	0.95[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs365108	0.88[CHB][hapmap]
rs3738246	0.98[ASN][1000 genomes]
rs3850855	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3850856	0.88[CHB][hapmap];1.00[ASN][1000 genomes]
rs415536	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4454584	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs454624	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4660295	1.00[ASN][1000 genomes]
rs4660834	0.88[CHB][hapmap];1.00[CHD][hapmap];0.98[ASN][1000 genomes]
rs4660839	0.85[CHB][hapmap];0.81[JPT][hapmap];1.00[ASN][1000 genomes]
rs4660841	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4660842	0.88[CHB][hapmap]
rs55932948	0.80[ASN][1000 genomes]
rs56086213	0.80[ASN][1000 genomes]
rs56363452	1.00[ASN][1000 genomes]
rs56791336	1.00[ASN][1000 genomes]
rs57754814	0.80[ASN][1000 genomes]
rs58374842	1.00[ASN][1000 genomes]
rs58934647	1.00[ASN][1000 genomes]
rs59220391	0.90[ASN][1000 genomes]
rs61789780	1.00[ASN][1000 genomes]
rs61789781	1.00[ASN][1000 genomes]
rs6429557	0.96[CEU][hapmap];0.88[CHB][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6688318	0.88[CHB][hapmap];1.00[CHD][hapmap];0.98[ASN][1000 genomes]
rs6702327	0.88[CHB][hapmap];0.98[ASN][1000 genomes]
rs72684493	1.00[ASN][1000 genomes]
rs7528534	0.80[CHD][hapmap]
rs974143	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	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	nsv546148	chr1:45500294-45627663	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs238249	PDZK1IP1	cis	cerebellum	SCAN
rs238249	MMACHC	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45525800-45558600	Weak transcription	HepG2	liver
2	chr1:45543800-45562200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:45544400-45560200	Weak transcription	Pancreas	Pancrea
4	chr1:45545000-45558200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:45550800-45562200	Weak transcription	Brain Germinal Matrix	brain
6	chr1:45551000-45558200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:45555400-45556000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr1:45555600-45556200	Weak transcription	Fetal Intestine Large	intestine

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