Variant report

Variant	rs11800409
Chromosome Location	chr1:93181013-93181014
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93175257..93178526-chr1:93178760..93181629,3	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11164803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11164816	0.83[EUR][1000 genomes]
rs11164820	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11577426	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11578004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578098	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11581176	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11581705	0.83[EUR][1000 genomes]
rs11583778	0.81[EUR][1000 genomes]
rs11585590	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586570	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11588545	0.83[EUR][1000 genomes]
rs11589122	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11589660	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11591094	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11800771	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11800848	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11801763	0.87[YRI][hapmap]
rs11803097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11805007	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11805229	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11805698	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807962	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11808092	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11809055	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11809700	0.94[EUR][1000 genomes]
rs11810217	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12728322	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12731107	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12733238	0.83[EUR][1000 genomes]
rs12738833	0.94[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12743005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743520	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12746893	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749480	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12756698	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12756786	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1333743	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1415296	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1854797	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs2051841	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2893226	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34202284	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34221961	0.83[EUR][1000 genomes]
rs34231012	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34244251	1.00[CHB][hapmap]
rs34250288	0.86[EUR][1000 genomes]
rs34288890	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34305407	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34343030	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34734076	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34761380	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34812295	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34843292	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35038369	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183060	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35241270	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35311203	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35435370	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35526187	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612297	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35699160	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35705463	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35901796	0.87[EUR][1000 genomes]
rs36099538	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36114576	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3790450	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4642892	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs56044027	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59864761	0.83[EUR][1000 genomes]
rs6604026	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs67026262	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67646822	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67876779	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs68160001	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71652503	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72724515	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72724555	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72724574	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72724586	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72724587	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7521417	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	esv1794348	chr1:93090476-93192932	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1802611	chr1:93090476-93219907	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv997898	chr1:93167128-93228156	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11800409	HFM1	cis	parietal	SCAN
rs11800409	FAM69A	cis	cerebellum	SCAN
rs11800409	MYEOV2	trans	cerebellum	SCAN
rs11800409	EPHX4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93098400-93205400	Weak transcription	NHLF	lung
2	chr1:93123600-93213400	Weak transcription	Gastric	stomach
3	chr1:93155800-93213400	Weak transcription	Lung	lung
4	chr1:93161000-93197400	Weak transcription	Primary B cells from cord blood	blood
5	chr1:93161000-93197800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:93161000-93199000	Weak transcription	Left Ventricle	heart
7	chr1:93163800-93190000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:93170200-93189800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr1:93174400-93202000	Weak transcription	Fetal Heart	heart
10	chr1:93175800-93190200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:93175800-93199400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:93176000-93183200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:93177800-93197600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:93178400-93181200	Weak transcription	Fetal Intestine Small	intestine
15	chr1:93180800-93181800	Flanking Active TSS	Liver	Liver
16	chr1:93181000-93181400	Active TSS	HepG2	liver

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