Variant report

Variant	rs6533237
Chromosome Location	chr4:106954292-106954293
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	chr4:106952681..106954677-chr4:106971571..106974056,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10000428	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10003024	0.83[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10004611	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10008428	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10008773	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10016884	0.85[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10017969	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10018910	0.85[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs10025052	0.81[EUR][1000 genomes]
rs10027207	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10030019	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs10049933	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11097912	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs11732251	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11732791	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11931386	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11932523	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11942153	0.82[EUR][1000 genomes]
rs12509366	0.82[EUR][1000 genomes]
rs12509640	0.91[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs12510966	0.91[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs12512683	0.81[EUR][1000 genomes]
rs12513345	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12642691	0.83[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12642900	0.82[EUR][1000 genomes]
rs13101612	0.83[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13113845	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13114479	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13121614	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13138528	0.89[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17272618	0.85[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs28391259	0.81[EUR][1000 genomes]
rs28394440	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28467469	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28784652	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28805707	0.87[ASN][1000 genomes]
rs28822186	0.83[EUR][1000 genomes]
rs28845843	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28897193	0.81[EUR][1000 genomes]
rs4306956	0.92[EUR][1000 genomes]
rs4307042	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4314353	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4355394	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4364267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374692	0.88[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4382109	0.89[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4470632	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4508971	0.94[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4569824	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4577583	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4600995	0.89[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55633564	0.82[EUR][1000 genomes]
rs60538413	0.95[EUR][1000 genomes]
rs62321365	0.82[EUR][1000 genomes]
rs6533242	0.83[EUR][1000 genomes]
rs6819081	0.89[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6823347	0.81[EUR][1000 genomes]
rs6824682	0.82[EUR][1000 genomes]
rs6828362	0.82[EUR][1000 genomes]
rs6836198	0.89[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6842919	0.96[EUR][1000 genomes]
rs6843331	0.95[EUR][1000 genomes]
rs6844105	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs6846579	0.91[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs6849573	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs6852388	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6853554	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs72677306	0.83[EUR][1000 genomes]
rs7438546	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7657962	0.91[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs7662592	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs7663321	0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs7667596	0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7668276	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7673101	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7677248	0.81[EUR][1000 genomes]
rs7678847	0.91[CEU][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7682646	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7687657	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7689298	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7692069	0.82[EUR][1000 genomes]
rs7692652	0.89[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap]
rs7693333	0.89[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7693448	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9685464	0.82[EUR][1000 genomes]
rs9991091	0.83[EUR][1000 genomes]
rs9996093	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][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	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522792	chr4:106895964-106982793	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6533237	SCYE1	Cis_1M	lymphoblastoid	RTeQTL
rs6533237	TBCK	cis	lymphoblastoid	seeQTL
rs6533237	TBCK	cis	parietal	SCAN
rs6533237	MGC16169	Cis_1M	lymphoblastoid	RTeQTL
rs6533237	ELOVL6	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106953600-106954400	Enhancers	HSMM	muscle
2	chr4:106953600-106956200	Enhancers	NHDF-Ad	bronchial
3	chr4:106953600-106956800	Enhancers	HSMMtube	muscle
4	chr4:106953800-106954600	Enhancers	Fetal Muscle Leg	muscle
5	chr4:106953800-106954800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:106953800-106954800	Enhancers	Osteobl	bone
7	chr4:106953800-106956000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr4:106953800-106957000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:106953800-106959600	Enhancers	HepG2	liver
10	chr4:106954000-106954400	Enhancers	Pancreas	Pancrea
11	chr4:106954000-106954800	Enhancers	Esophagus	oesophagus
12	chr4:106954000-106956000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:106954000-106956200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:106954000-106956200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:106954200-106955000	Enhancers	NH-A	brain
16	chr4:106954200-106956400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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