Variant report

Variant	rs11600640
Chromosome Location	chr11:75201091-75201092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11236444	1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12421913	0.81[CHB][hapmap]
rs2187568	0.99[ASN][1000 genomes]
rs2276443	0.90[CHB][hapmap]
rs55955041	0.88[ASN][1000 genomes]
rs56010007	0.81[ASN][1000 genomes]
rs56386896	0.99[ASN][1000 genomes]
rs56412430	0.88[ASN][1000 genomes]
rs56851635	0.93[ASN][1000 genomes]
rs61897380	0.81[ASN][1000 genomes]
rs61897406	0.88[ASN][1000 genomes]
rs61897410	0.96[ASN][1000 genomes]
rs61897411	0.96[ASN][1000 genomes]
rs61897413	0.81[ASN][1000 genomes]
rs61897414	0.99[ASN][1000 genomes]
rs61897415	0.99[ASN][1000 genomes]
rs61897416	0.97[ASN][1000 genomes]
rs61897419	0.93[ASN][1000 genomes]
rs7125082	0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[ASN][1000 genomes]
rs7128197	0.87[ASN][1000 genomes]
rs7131225	0.89[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs73494872	0.87[ASN][1000 genomes]

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
rs11600640	NDUFC2	cis	parietal	SCAN
rs11600640	GDPD5	cis	multi-tissue	Pritchard
rs11600640	GDPD5	cis	lymphoblastoid	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

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	chr11:75187600-75202000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:75188000-75201600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr11:75188400-75201200	Weak transcription	HSMM	muscle
11	chr11:75188400-75201400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:75188400-75201400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:75188400-75201600	Weak transcription	HSMMtube	muscle
14	chr11:75188600-75201600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr11:75190400-75207400	Weak transcription	Fetal Stomach	stomach
16	chr11:75190800-75201600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:75192200-75202800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr11:75193000-75203200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:75193800-75203200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr11:75194000-75203000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:75194600-75203000	Weak transcription	Lung	lung
22	chr11:75195000-75201200	Weak transcription	Spleen	Spleen
23	chr11:75196400-75202200	Strong transcription	Fetal Intestine Small	intestine
24	chr11:75197800-75201400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr11:75197800-75201600	Enhancers	Brain Germinal Matrix	brain
26	chr11:75198200-75201400	Strong transcription	Fetal Intestine Large	intestine
27	chr11:75198200-75203000	Weak transcription	Hela-S3	cervix
28	chr11:75198400-75201200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:75198400-75201200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:75198600-75203600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr11:75199000-75201200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr11:75199000-75201200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:75199000-75201800	Strong transcription	HepG2	liver
34	chr11:75199200-75202800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr11:75199400-75201400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:75199400-75207000	Weak transcription	Adipose Nuclei	Adipose
37	chr11:75199400-75209800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr11:75199600-75201600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:75200000-75201400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:75200000-75202600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr11:75200000-75219600	Weak transcription	Fetal Brain Female	brain
42	chr11:75200200-75203200	Weak transcription	Psoas Muscle	Psoas
43	chr11:75200400-75201400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr11:75200400-75202400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:75201000-75201200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr11:75201000-75201400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr11:75201000-75201400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:75201000-75202000	Enhancers	Placenta Amnion	Placenta Amnion
49	chr11:75201000-75202200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:75201000-75202400	Enhancers	H1 Cell Line	embryonic stem cell

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