Variant report

Variant	rs11039114
Chromosome Location	chr11:47185680-47185681
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47179475..47181210-chr11:47184967..47187078,2	MCF-7	breast:
2	chr11:47184473..47185977-chr6:26123417..26125817,2	K562	blood:
3	chr11:47183256..47186030-chr11:47281970..47284554,2	MCF-7	breast:
4	chr11:46890949..46892684-chr11:47183314..47186093,2	K562	blood:
5	chr11:47185316..47187006-chr17:58634417..58637411,2	MCF-7	breast:
6	chr11:47182976..47185487-chr11:47185518..47189747,4	MCF-7	breast:
7	chr11:47176348..47178224-chr11:47185293..47188253,2	K562	blood:
8	chr11:47183888..47186311-chr11:47279921..47282394,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000025434	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000149179	Chromatin interaction
ENSG00000180596	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11039106	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039149	1.00[ASW][hapmap]
rs2867972	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3740691	0.95[GIH][hapmap]
rs3740694	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];1.00[ASN][1000 genomes]
rs4752817	0.94[CEU][hapmap]
rs7130989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs752849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7940473	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948786	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11039114	ARFGAP2	cis	cerebellum	SCAN
rs11039114	MTCH2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47165400-47188600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:47171400-47186000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr11:47171600-47186400	Weak transcription	Psoas Muscle	Psoas
4	chr11:47175200-47185800	Weak transcription	Small Intestine	intestine
5	chr11:47175200-47186400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:47175200-47188600	Weak transcription	Fetal Heart	heart
7	chr11:47175400-47186000	Weak transcription	HUVEC	blood vessel
8	chr11:47175400-47186600	Weak transcription	Fetal Kidney	kidney
9	chr11:47175400-47197600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:47176000-47196600	Strong transcription	Fetal Intestine Small	intestine
11	chr11:47176200-47187800	Weak transcription	NHDF-Ad	bronchial
12	chr11:47176600-47188600	Weak transcription	Fetal Brain Male	brain
13	chr11:47176800-47193000	Strong transcription	Fetal Brain Female	brain
14	chr11:47176800-47196600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:47177000-47186200	Weak transcription	GM12878-XiMat	blood
16	chr11:47177400-47186200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:47177400-47187000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:47178000-47186400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr11:47178000-47186400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr11:47178000-47197000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:47178200-47194000	Strong transcription	Dnd41	blood
22	chr11:47178400-47186200	Weak transcription	HSMMtube	muscle
23	chr11:47178800-47196800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:47180000-47186000	Weak transcription	Fetal Lung	lung
25	chr11:47180600-47196600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr11:47180800-47186200	Weak transcription	Stomach Mucosa	stomach
27	chr11:47180800-47188600	Weak transcription	K562	blood
28	chr11:47181400-47197000	Weak transcription	Right Atrium	heart
29	chr11:47182000-47196400	Strong transcription	Hela-S3	cervix
30	chr11:47182200-47193400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:47182200-47194800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:47182200-47197000	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr11:47182400-47187200	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr11:47182400-47196400	Strong transcription	Fetal Intestine Large	intestine
35	chr11:47183200-47185800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:47183200-47186000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr11:47183200-47186800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr11:47183200-47194000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr11:47183200-47197000	Strong transcription	Placenta	Placenta
40	chr11:47183200-47197200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:47183400-47186600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
42	chr11:47183400-47190400	Strong transcription	Brain Hippocampus Middle	brain
43	chr11:47183400-47190600	Strong transcription	Gastric	stomach
44	chr11:47183400-47192600	Strong transcription	Primary T cells from cord blood	blood
45	chr11:47183400-47192800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr11:47183400-47193000	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr11:47183400-47193200	Strong transcription	Brain Cingulate Gyrus	brain
48	chr11:47183400-47193800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr11:47183400-47194600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:47183400-47194600	Strong transcription	Colonic Mucosa	Colon

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