Variant report

Variant	rs3012185
Chromosome Location	chr1:224854316-224854317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224847963..224850849-chr1:224853050..224855048,2	K562	blood:
2	chr1:224845828..224850849-chr1:224853050..224856939,4	K562	blood:

Variant related genes	Relation type
ENSG00000234247	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10429870	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10799277	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs10799590	0.95[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10915684	0.87[ASW][hapmap];0.91[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10915687	0.95[ASN][1000 genomes]
rs10915694	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs10915696	1.00[CEU][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10915698	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10915699	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10915704	1.00[YRI][hapmap]
rs12025142	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12092438	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12121558	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs12124262	0.95[CEU][hapmap]
rs12130499	0.95[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12132665	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13374487	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs1369847	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1436169	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1436171	0.84[CEU][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1436172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1465768	0.84[CEU][hapmap];0.80[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1603917	0.87[ASW][hapmap];0.95[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1603918	0.95[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs169888	0.91[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1965777	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2405516	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2405525	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2648746	0.95[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2897161	0.80[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2936575	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs298732	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs298733	1.00[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs298734	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs298735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298738	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs298739	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2993124	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147293	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653402	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653404	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653591	0.87[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653592	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56881651	0.85[EUR][1000 genomes]
rs61676104	0.84[EUR][1000 genomes]
rs6667034	0.95[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6686604	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6686633	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67817586	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs713098	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7511897	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7521396	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7535296	0.93[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7537973	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7542431	0.85[EUR][1000 genomes]
rs7542995	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs7543218	0.95[EUR][1000 genomes]
rs7544312	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7545574	1.00[CEU][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs873594	0.84[CEU][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3012185	DEGS1	cis	cerebellum	SCAN
rs3012185	RAB3GAP2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224832200-224884400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:224832800-224869000	Weak transcription	Dnd41	blood
3	chr1:224833200-224874400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:224840800-224856800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:224840800-224858000	Weak transcription	NH-A	brain
6	chr1:224841000-224856600	Weak transcription	Pancreas	Pancrea
7	chr1:224851400-224863000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:224853200-224854800	Enhancers	Psoas Muscle	Psoas
9	chr1:224853400-224855600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:224853400-224856200	Weak transcription	NHDF-Ad	bronchial
11	chr1:224853600-224854800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:224853600-224857400	Enhancers	Fetal Brain Male	brain
13	chr1:224854000-224856200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:224854000-224856200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:224854200-224856600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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