Variant report

Variant	rs11253227
Chromosome Location	chr10:5594362-5594363
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5496908..5513504-chr10:5583876..5597686,82	MCF-7	breast:
2	chr10:5585944..5594625-chr10:5661457..5667151,17	MCF-7	breast:
3	chr10:5593662..5595801-chr10:5669870..5671896,3	MCF-7	breast:
4	chr10:5583637..5601494-chr10:5650599..5672411,88	MCF-7	breast:
5	chr10:5593662..5596441-chr10:5715811..5718225,2	MCF-7	breast:
6	chr10:5491451..5493035-chr10:5593759..5595362,2	K562	blood:
7	chr10:5592839..5594625-chr10:5635555..5637681,2	MCF-7	breast:
8	chr10:5584975..5598212-chr10:5621607..5634806,86	MCF-7	breast:
9	chr10:5588926..5596967-chr10:5614767..5621599,13	MCF-7	breast:
10	chr10:5593038..5596682-chr10:5605799..5608006,4	MCF-7	breast:
11	chr10:5592831..5595725-chr10:5854017..5855784,2	MCF-7	breast:
12	chr10:5485039..5496687-chr10:5584772..5598184,85	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231483	Chromatin interaction
ENSG00000057608	Chromatin interaction
ENSG00000173848	Chromatin interaction
ENSG00000228685	Chromatin interaction
ENSG00000228951	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11253225	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11253226	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12571911	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4242799	0.89[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7079395	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs7900685	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv932104	chr10:5203626-5641023	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv549886	chr10:5205437-5632060	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv1054865	chr10:5225305-5638119	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv831774	chr10:5463556-5657421	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv894798	chr10:5503610-5670275	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv1051283	chr10:5505474-5619941	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1049523	chr10:5542109-5619941	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv523491	chr10:5542109-5720067	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv1052002	chr10:5544571-5619941	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv1038479	chr10:5545773-5619941	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	esv2757364	chr10:5557024-5720512	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
13	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	nsv894800	chr10:5572893-5621628	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv470915	chr10:5591025-5602880	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11253227	IL2RA	cis	lymphoblastoid	seeQTL
rs11253227	IL15RA	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5586200-5596600	Enhancers	Placenta	Placenta
2	chr10:5586200-5597000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:5586400-5597800	Enhancers	Esophagus	oesophagus
4	chr10:5587000-5597600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:5587600-5596800	Enhancers	Fetal Thymus	thymus
6	chr10:5587800-5594400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr10:5588400-5608200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:5589400-5597000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr10:5590200-5596800	Enhancers	HMEC	breast
10	chr10:5590200-5597200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr10:5590200-5599400	Enhancers	Fetal Intestine Small	intestine
12	chr10:5590200-5599800	Enhancers	Fetal Intestine Large	intestine
13	chr10:5590400-5596200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr10:5590400-5597000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:5590600-5595600	Weak transcription	Small Intestine	intestine
16	chr10:5590600-5596200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr10:5590600-5596200	Weak transcription	Brain Angular Gyrus	brain
18	chr10:5590600-5596400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr10:5590800-5595600	Weak transcription	Ovary	ovary
20	chr10:5590800-5596000	Weak transcription	Colon Smooth Muscle	Colon
21	chr10:5590800-5597400	Enhancers	Stomach Mucosa	stomach
22	chr10:5590800-5598400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr10:5591000-5594400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr10:5591000-5594400	Weak transcription	Spleen	Spleen
25	chr10:5591000-5595400	Weak transcription	Brain Anterior Caudate	brain
26	chr10:5591000-5596000	Weak transcription	Adipose Nuclei	Adipose
27	chr10:5591000-5596000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr10:5591000-5596200	Weak transcription	Psoas Muscle	Psoas
29	chr10:5591000-5596400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:5591000-5598600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:5591200-5595800	Weak transcription	Liver	Liver
32	chr10:5591200-5596200	Weak transcription	Fetal Brain Male	brain
33	chr10:5591400-5594600	Enhancers	Hela-S3	cervix
34	chr10:5591400-5595400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr10:5591400-5596000	Weak transcription	Pancreas	Pancrea
36	chr10:5591400-5596200	Enhancers	HepG2	liver
37	chr10:5591400-5597200	Enhancers	K562	blood
38	chr10:5591400-5605400	Weak transcription	Right Atrium	heart
39	chr10:5591800-5595200	Weak transcription	HUVEC	blood vessel
40	chr10:5591800-5595600	Weak transcription	Lung	lung
41	chr10:5591800-5596000	Weak transcription	NHLF	lung
42	chr10:5591800-5596200	Weak transcription	NHDF-Ad	bronchial
43	chr10:5592200-5594600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr10:5592400-5595200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr10:5592400-5596400	Enhancers	Colonic Mucosa	Colon
46	chr10:5592600-5595200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr10:5592800-5594600	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr10:5592800-5595800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr10:5592800-5596600	Enhancers	HSMM	muscle
50	chr10:5592800-5596600	Enhancers	NH-A	brain

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