Variant report

Variant	rs11236444
Chromosome Location	chr11:75219291-75219292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75218597..75220544-chr11:75272386..75274984,2	MCF-7	breast:
2	chr11:75218923..75220446-chr11:75235371..75237646,2	K562	blood:
3	chr11:75187397..75189556-chr11:75217050..75219601,2	K562	blood:
4	chr11:75160860..75162731-chr11:75218934..75220538,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL35-1	chr11:75219212-75219436	ENSG00000254460.1

Variant related genes	Relation type
ENSG00000149257	Chromatin interaction
ENSG00000158555	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11600640	1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12421913	0.81[CHB][hapmap]
rs2187568	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276443	0.89[CEU][hapmap];0.90[CHB][hapmap];0.85[LWK][hapmap];0.84[EUR][1000 genomes]
rs55955041	0.90[EUR][1000 genomes]
rs56010007	0.84[EUR][1000 genomes]
rs56207324	0.84[EUR][1000 genomes]
rs56386896	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56412430	0.90[EUR][1000 genomes]
rs56851635	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61897374	0.84[EUR][1000 genomes]
rs61897380	0.84[EUR][1000 genomes]
rs61897406	0.86[EUR][1000 genomes]
rs61897410	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61897411	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61897413	0.87[EUR][1000 genomes]
rs61897414	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61897415	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61897416	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61897419	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7125082	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[EUR][1000 genomes]
rs7128197	0.86[EUR][1000 genomes]
rs7131225	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs73494872	0.81[EUR][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11236444	GDPD5	cis	lymphoblastoid	seeQTL
rs11236444	GDPD5	cis	multi-tissue	Pritchard

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75200000-75219600	Weak transcription	Fetal Brain Female	brain
2	chr11:75210400-75219400	Weak transcription	Pancreas	Pancrea
3	chr11:75211200-75219800	Weak transcription	Esophagus	oesophagus
4	chr11:75212600-75227400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:75215600-75219400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:75215600-75223600	Enhancers	Adipose Nuclei	Adipose
7	chr11:75215800-75222000	Enhancers	Fetal Intestine Large	intestine
8	chr11:75216000-75222600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:75216200-75233600	Genic enhancers	Fetal Intestine Small	intestine
10	chr11:75216400-75219800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr11:75216400-75221600	Enhancers	Fetal Muscle Leg	muscle
12	chr11:75216400-75221800	Enhancers	Fetal Muscle Trunk	muscle
13	chr11:75216400-75222000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr11:75216600-75219800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:75217000-75220600	Enhancers	Lung	lung
16	chr11:75217000-75221600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr11:75217400-75219800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:75217400-75220400	Enhancers	HSMMtube	muscle
19	chr11:75217800-75221600	Enhancers	Primary B cells from peripheral blood	blood
20	chr11:75217800-75221600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr11:75217800-75221800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr11:75217800-75222600	Enhancers	Placenta	Placenta
23	chr11:75217800-75234800	Weak transcription	Ovary	ovary
24	chr11:75218000-75219600	Weak transcription	Brain Hippocampus Middle	brain
25	chr11:75218000-75220600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:75218000-75221400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr11:75218000-75223400	Enhancers	HepG2	liver
28	chr11:75218200-75220400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr11:75218200-75220400	Enhancers	Fetal Thymus	thymus
30	chr11:75218200-75221400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr11:75218200-75221800	Enhancers	Primary T cells fromperipheralblood	blood
32	chr11:75218200-75222200	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr11:75218400-75219800	Enhancers	Spleen	Spleen
34	chr11:75218400-75220000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr11:75218400-75220200	Enhancers	GM12878-XiMat	blood
36	chr11:75218400-75220400	Enhancers	Primary T cells from cord blood	blood
37	chr11:75218400-75220600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr11:75218400-75220600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:75218400-75220600	Enhancers	Hela-S3	cervix
40	chr11:75218400-75221200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr11:75218400-75221800	Weak transcription	Fetal Stomach	stomach
42	chr11:75218600-75220000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr11:75218600-75220400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr11:75218600-75220400	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr11:75218600-75220600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr11:75218600-75221600	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr11:75218800-75220200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr11:75218800-75220400	Enhancers	Fetal Brain Male	brain
49	chr11:75218800-75224400	Weak transcription	Right Ventricle	heart
50	chr11:75219000-75219600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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