Variant report

Variant	rs668727
Chromosome Location	chr11:75200991-75200992
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1004856	0.85[YRI][hapmap];0.88[AFR][1000 genomes]
rs10751243	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11236441	0.82[AFR][1000 genomes]
rs1540211	0.80[YRI][hapmap]
rs1557471	0.86[YRI][hapmap]
rs1557474	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1623440	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1631470	0.89[YRI][hapmap]
rs1631865	0.88[CEU][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790145	0.82[ASW][hapmap];0.91[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790149	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790153	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790154	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790155	0.96[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1790156	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790158	0.92[CEU][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790160	0.86[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1793396	0.88[JPT][hapmap]
rs1793398	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs1793411	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1793412	0.88[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1793414	0.89[YRI][hapmap];0.90[AFR][1000 genomes]
rs1793415	0.96[CEU][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1894213	0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs471857	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs473462	0.85[EUR][1000 genomes]
rs474056	0.84[EUR][1000 genomes]
rs482458	0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs482503	0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs486326	0.84[EUR][1000 genomes]
rs488305	0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs492309	0.83[EUR][1000 genomes]
rs504685	0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs518611	0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs523617	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs532454	0.83[EUR][1000 genomes]
rs535520	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs535523	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs546632	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs547844	0.85[EUR][1000 genomes]
rs550957	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609793	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs611449	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs623338	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs625938	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs628972	0.89[ASW][hapmap];0.87[LWK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs653673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125082	0.80[JPT][hapmap]

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	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	nsv897923	chr11:75129007-75302855	Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv825996	chr11:75195626-75203332	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2757452	chr11:75198280-75201091	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv2759838	chr11:75198280-75201091	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs668727	PLEKHB1	cis	parietal	SCAN
rs668727	GDPD5	cis	multi-tissue	Pritchard
rs668727	ARAP1	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75187000-75201400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:75187200-75201200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr11:75187200-75203000	Weak transcription	Primary T cells from cord blood	blood
4	chr11:75187400-75202800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr11:75187400-75202800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:75187400-75202800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:75187400-75203000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr11:75187600-75201000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:75187600-75202000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:75187800-75201000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:75188000-75201600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr11:75188400-75201200	Weak transcription	HSMM	muscle
13	chr11:75188400-75201400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:75188400-75201400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:75188400-75201600	Weak transcription	HSMMtube	muscle
16	chr11:75188600-75201600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr11:75190400-75207400	Weak transcription	Fetal Stomach	stomach
18	chr11:75190800-75201600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:75192200-75202800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr11:75193000-75203200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr11:75193800-75203200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr11:75194000-75203000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:75194600-75203000	Weak transcription	Lung	lung
24	chr11:75195000-75201200	Weak transcription	Spleen	Spleen
25	chr11:75196400-75202200	Strong transcription	Fetal Intestine Small	intestine
26	chr11:75197800-75201400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr11:75197800-75201600	Enhancers	Brain Germinal Matrix	brain
28	chr11:75198000-75201000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:75198200-75201400	Strong transcription	Fetal Intestine Large	intestine
30	chr11:75198200-75203000	Weak transcription	Hela-S3	cervix
31	chr11:75198400-75201200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:75198400-75201200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:75198600-75203600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:75199000-75201200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr11:75199000-75201200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr11:75199000-75201800	Strong transcription	HepG2	liver
37	chr11:75199200-75202800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr11:75199400-75201400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr11:75199400-75207000	Weak transcription	Adipose Nuclei	Adipose
40	chr11:75199400-75209800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr11:75199600-75201600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:75200000-75201000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:75200000-75201400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:75200000-75202600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:75200000-75219600	Weak transcription	Fetal Brain Female	brain
46	chr11:75200200-75203200	Weak transcription	Psoas Muscle	Psoas
47	chr11:75200400-75201000	Genic enhancers	Placenta	Placenta
48	chr11:75200400-75201400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr11:75200400-75202400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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