Variant report

Variant	rs11124680
Chromosome Location	chr2:39620013-39620014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39619324..39621910-chr2:39662875..39665257,2	K562	blood:

Variant related genes	Relation type
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1012689	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10175094	0.84[CHB][hapmap]
rs10185961	0.80[CEU][hapmap];0.84[CHB][hapmap]
rs10193807	0.87[ASN][1000 genomes]
rs10865148	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11124671	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs11124675	0.94[CEU][hapmap];0.92[CHB][hapmap];0.85[EUR][1000 genomes]
rs11677383	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs11677611	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11688033	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11695072	0.87[JPT][hapmap]
rs12151392	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs12162306	0.82[ASN][1000 genomes]
rs12617901	0.91[CHB][hapmap]
rs12618944	0.81[ASN][1000 genomes]
rs12624242	0.81[JPT][hapmap]
rs12712634	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs12712640	0.85[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12712642	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712643	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1558854	0.81[ASN][1000 genomes]
rs1861733	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs1861734	0.91[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2024514	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs3755171	0.81[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3755172	0.82[ASN][1000 genomes]
rs3755176	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs3770662	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs3770664	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3770671	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs3770672	0.81[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap]
rs3770673	0.81[ASN][1000 genomes]
rs3887311	0.82[ASN][1000 genomes]
rs4670932	0.92[AFR][1000 genomes]
rs6544214	0.84[CHB][hapmap]
rs6709424	0.84[CHB][hapmap]
rs6714566	0.81[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap]
rs6719469	0.84[ASN][1000 genomes]
rs7340455	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7421175	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7561630	0.90[ASN][1000 genomes]
rs7569492	0.80[ASN][1000 genomes]
rs7573923	0.81[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap]
rs7581692	0.86[ASN][1000 genomes]
rs7582848	0.81[ASN][1000 genomes]
rs7594145	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7595469	0.82[ASN][1000 genomes]
rs7598583	0.93[JPT][hapmap]
rs7605427	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7608958	0.81[ASN][1000 genomes]
rs9037	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs9309036	0.84[ASN][1000 genomes]
rs9309037	0.81[CEU][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
2	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
4	chr2:39603400-39625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:39603400-39626800	Weak transcription	Primary T cells from cord blood	blood
6	chr2:39607000-39626800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:39607400-39624800	Weak transcription	Stomach Mucosa	stomach
8	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:39608000-39622800	Weak transcription	Fetal Kidney	kidney
10	chr2:39608400-39621000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:39608400-39626200	Weak transcription	Brain Substantia Nigra	brain
12	chr2:39609200-39621600	Weak transcription	Lung	lung
13	chr2:39609400-39621200	Weak transcription	Brain Angular Gyrus	brain
14	chr2:39609400-39621200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:39609400-39621600	Weak transcription	HSMM	muscle
16	chr2:39609600-39621200	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:39609600-39621400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:39609600-39621600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:39609600-39621600	Weak transcription	NH-A	brain
20	chr2:39609600-39621600	Weak transcription	Osteobl	bone
21	chr2:39609600-39626400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:39610000-39621200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:39610200-39621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:39610200-39626400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:39613000-39621400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:39613400-39621200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:39613600-39621600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:39613600-39621600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:39613800-39630600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:39614000-39628000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:39614800-39620800	Weak transcription	Right Ventricle	heart
32	chr2:39614800-39621600	Weak transcription	Pancreas	Pancrea
33	chr2:39615600-39621400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:39615800-39621200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:39615800-39626800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:39616000-39620200	Weak transcription	Fetal Lung	lung
37	chr2:39616000-39620800	Weak transcription	Left Ventricle	heart
38	chr2:39616000-39621200	Weak transcription	Aorta	Aorta
39	chr2:39616000-39622200	Weak transcription	Fetal Stomach	stomach
40	chr2:39616000-39626400	Weak transcription	Gastric	stomach
41	chr2:39616800-39621200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:39617400-39620400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:39617600-39621200	Weak transcription	Fetal Heart	heart
44	chr2:39617600-39626200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr2:39617600-39626400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:39617800-39620800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:39617800-39621200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:39617800-39621200	Weak transcription	NHLF	lung
49	chr2:39617800-39621400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:39617800-39621400	Weak transcription	NHDF-Ad	bronchial

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