Variant report

Variant	rs11229539
Chromosome Location	chr11:58354927-58354928
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58344637..58348325-chr11:58354082..58356724,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255073	Chromatin interaction
ENSG00000110031	Chromatin interaction
ENSG00000186660	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10160409	1.00[YRI][hapmap]
rs11229437	1.00[YRI][hapmap]
rs11229466	1.00[AFR][1000 genomes]
rs11229507	1.00[YRI][hapmap]
rs11229508	1.00[YRI][hapmap]
rs11229520	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11229523	1.00[YRI][hapmap]
rs11229525	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11229546	1.00[YRI][hapmap]
rs11229547	1.00[YRI][hapmap]
rs11229570	1.00[AFR][1000 genomes]
rs11229571	1.00[AFR][1000 genomes]
rs12271331	0.89[AFR][1000 genomes]
rs12272722	1.00[AFR][1000 genomes]
rs12276093	1.00[YRI][hapmap]
rs12278099	0.90[AFR][1000 genomes]
rs12281441	1.00[AFR][1000 genomes]
rs12282241	0.89[AFR][1000 genomes]
rs12282490	1.00[YRI][hapmap]
rs12282535	1.00[YRI][hapmap]
rs12282976	1.00[YRI][hapmap]
rs12285076	1.00[AFR][1000 genomes]
rs12286542	1.00[AFR][1000 genomes]
rs12293904	0.89[AFR][1000 genomes]
rs12295771	1.00[YRI][hapmap];1.00[AFR][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	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58347600-58360200	Weak transcription	Esophagus	oesophagus
2	chr11:58347600-58361400	Weak transcription	Gastric	stomach
3	chr11:58347600-58379600	Weak transcription	Pancreas	Pancrea
4	chr11:58347600-58379800	Weak transcription	Lung	lung
5	chr11:58347600-58380200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:58347800-58377200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr11:58347800-58380200	Weak transcription	Aorta	Aorta
8	chr11:58348200-58377400	Weak transcription	Fetal Kidney	kidney
9	chr11:58348600-58360200	Weak transcription	Stomach Mucosa	stomach
10	chr11:58349000-58358200	Weak transcription	Ovary	ovary
11	chr11:58349000-58359200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr11:58349000-58359800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:58349000-58360000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr11:58349000-58360200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr11:58349200-58359200	Weak transcription	Fetal Muscle Leg	muscle
16	chr11:58349200-58359200	Weak transcription	Fetal Stomach	stomach
17	chr11:58349200-58360200	Weak transcription	Left Ventricle	heart
18	chr11:58349200-58363200	Weak transcription	Brain Germinal Matrix	brain
19	chr11:58349200-58377400	Weak transcription	HSMMtube	muscle
20	chr11:58349200-58379600	Weak transcription	Spleen	Spleen
21	chr11:58349200-58380600	Weak transcription	Fetal Brain Male	brain
22	chr11:58349200-58384200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:58349200-58384800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:58349400-58359200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:58349400-58360000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:58349400-58367600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:58349600-58360000	Weak transcription	Fetal Intestine Small	intestine
28	chr11:58349600-58360000	Weak transcription	Thymus	Thymus
29	chr11:58349600-58360200	Weak transcription	Fetal Heart	heart
30	chr11:58349600-58364200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr11:58349600-58368200	Weak transcription	Brain Anterior Caudate	brain
32	chr11:58349800-58359000	Weak transcription	NHLF	lung
33	chr11:58350200-58359200	Weak transcription	Small Intestine	intestine
34	chr11:58350800-58359000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:58351000-58360400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr11:58351000-58361400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr11:58351000-58367800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr11:58351200-58378200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:58351400-58357600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr11:58351800-58360000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr11:58352000-58355000	Strong transcription	Fetal Thymus	thymus
42	chr11:58352000-58355000	Genic enhancers	HepG2	liver
43	chr11:58352000-58355200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:58352000-58355400	Strong transcription	HMEC	breast
45	chr11:58352000-58355600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr11:58352000-58355800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
47	chr11:58352000-58356400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:58352000-58356400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr11:58352000-58368400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:58352200-58355000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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