Variant report

Variant	rs499974
Chromosome Location	chr11:75455021-75455022
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	chr11:75447941..75450758-chr11:75453303..75455512,2	MCF-7	breast:
2	chr11:75446630..75448572-chr11:75453291..75455245,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10160784	0.93[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1017713	0.81[CHB][hapmap]
rs10219339	0.81[CHB][hapmap]
rs10793124	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs10793125	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs10793126	0.88[ASN][1000 genomes]
rs10793127	0.80[ASN][1000 genomes]
rs10899105	0.81[ASN][1000 genomes]
rs10899109	0.88[ASN][1000 genomes]
rs10899110	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs10899113	0.80[ASN][1000 genomes]
rs10899116	0.81[CHB][hapmap]
rs10899119	0.81[CHB][hapmap]
rs10899121	0.81[CHB][hapmap]
rs10899122	0.81[CHB][hapmap]
rs10899123	0.81[CHB][hapmap]
rs11236507	0.80[ASN][1000 genomes]
rs11236508	0.81[ASN][1000 genomes]
rs11236509	0.81[ASN][1000 genomes]
rs11236511	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs11236514	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs11236515	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs11236516	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs11236517	0.87[CHB][hapmap];0.86[ASN][1000 genomes]
rs11236518	0.87[CHB][hapmap];0.88[ASN][1000 genomes]
rs11236519	0.80[ASN][1000 genomes]
rs11236527	0.80[ASN][1000 genomes]
rs11236528	0.80[ASN][1000 genomes]
rs11236530	0.81[CHB][hapmap]
rs11236531	0.81[CHB][hapmap]
rs11236534	0.81[CHB][hapmap]
rs11821808	0.88[ASN][1000 genomes]
rs11823410	0.92[GIH][hapmap]
rs11823869	0.81[CHB][hapmap]
rs1219549	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1219550	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12222542	0.81[CHB][hapmap]
rs12222995	0.81[CHB][hapmap]
rs2008476	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs36016715	0.80[ASN][1000 genomes]
rs498936	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs531117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543886	0.81[GIH][hapmap]
rs559355	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575976	0.81[GIH][hapmap]
rs58411334	0.80[ASN][1000 genomes]
rs600518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609379	0.92[GIH][hapmap]
rs643884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656095	0.81[AMR][1000 genomes]
rs673335	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs695110	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72995678	0.81[ASN][1000 genomes]
rs72997616	0.80[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	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv897924	chr11:75424546-75678647	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
HDL cholesterol	24097068	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs499974	ARAP1	cis	parietal	SCAN
rs499974	AQP11	cis	parietal	SCAN
rs499974	DGAT2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75452800-75456000	Enhancers	Liver	Liver
2	chr11:75453200-75455200	Enhancers	Stomach Mucosa	stomach
3	chr11:75453200-75455600	Enhancers	Fetal Intestine Small	intestine
4	chr11:75453600-75455200	Enhancers	Duodenum Mucosa	Duodenum
5	chr11:75453800-75455600	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr11:75453800-75456200	Enhancers	Fetal Intestine Large	intestine
7	chr11:75453800-75458000	Enhancers	Fetal Heart	heart
8	chr11:75454000-75455600	Enhancers	K562	blood
9	chr11:75454000-75456400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:75454000-75456800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr11:75454000-75457000	Enhancers	Left Ventricle	heart
12	chr11:75454200-75455400	Enhancers	Fetal Muscle Leg	muscle
13	chr11:75454200-75455600	Enhancers	Fetal Muscle Trunk	muscle
14	chr11:75454600-75456400	Enhancers	Adipose Nuclei	Adipose
15	chr11:75454800-75455200	Enhancers	Psoas Muscle	Psoas
16	chr11:75454800-75455200	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr11:75454800-75455400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:75454800-75455400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:75454800-75455400	Bivalent Enhancer	Fetal Stomach	stomach
20	chr11:75454800-75455400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr11:75454800-75455400	Enhancers	Spleen	Spleen
22	chr11:75454800-75455600	Flanking Active TSS	HepG2	liver
23	chr11:75454800-75455800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr11:75454800-75456000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:75454800-75456000	Enhancers	Fetal Thymus	thymus
26	chr11:75454800-75457400	Enhancers	Right Atrium	heart
27	chr11:75454800-75458200	Enhancers	Right Ventricle	heart
28	chr11:75455000-75455200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr11:75455000-75455200	Enhancers	Placenta	Placenta
30	chr11:75455000-75455400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:75455000-75455400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr11:75455000-75455400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
33	chr11:75455000-75455400	Bivalent Enhancer	NHEK	skin
34	chr11:75455000-75455600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:75455000-75455600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:75455000-75455600	Enhancers	Esophagus	oesophagus

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