Variant report

Variant	rs11124737
Chromosome Location	chr2:40471407-40471408
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40440228..40440936-chr2:40471245..40471990,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10180584	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10490208	0.82[CHD][hapmap]
rs11674102	0.83[GIH][hapmap]
rs17504670	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs4581943	0.93[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4952401	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs4952594	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs4952599	0.81[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56410612	0.93[ASN][1000 genomes]
rs6716847	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6737759	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7593406	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7602176	0.93[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs877099	0.82[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs918050	0.86[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv524586	chr2:40447587-40497501	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv873912	chr2:40468418-40492315	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv873913	chr2:40469705-40485074	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11124737	THADA	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40448000-40487400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:40451400-40490000	Weak transcription	Dnd41	blood
3	chr2:40467800-40487400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:40468000-40472000	Weak transcription	Fetal Lung	lung
5	chr2:40468000-40476600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:40468600-40472000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:40468800-40472600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr2:40469000-40472200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr2:40469000-40475200	Enhancers	Fetal Heart	heart
10	chr2:40469200-40472000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr2:40469200-40472200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr2:40469200-40472200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr2:40469400-40472200	Enhancers	HSMMtube	muscle
14	chr2:40469600-40472600	Enhancers	Colon Smooth Muscle	Colon
15	chr2:40469600-40472800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:40469800-40474400	Enhancers	Rectal Smooth Muscle	rectum
17	chr2:40470000-40472400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:40470000-40473200	Enhancers	NHDF-Ad	bronchial
19	chr2:40470200-40472400	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr2:40470400-40471800	Enhancers	H9 Cell Line	embryonic stem cell
21	chr2:40470400-40472000	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr2:40470400-40472000	Enhancers	Fetal Muscle Leg	muscle
23	chr2:40470400-40472400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:40470400-40472400	Enhancers	NHLF	lung
25	chr2:40470400-40472600	Enhancers	HSMM	muscle
26	chr2:40470400-40481200	Weak transcription	Brain Germinal Matrix	brain
27	chr2:40470600-40471600	Enhancers	Small Intestine	intestine
28	chr2:40470600-40471600	Flanking Active TSS	NH-A	brain
29	chr2:40470600-40472000	Enhancers	Fetal Stomach	stomach
30	chr2:40470600-40472200	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr2:40470600-40472200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:40470600-40472400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:40470800-40472000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr2:40470800-40472200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:40470800-40472200	Enhancers	Left Ventricle	heart
36	chr2:40470800-40472400	Enhancers	Hela-S3	cervix
37	chr2:40470800-40474800	Enhancers	Fetal Intestine Small	intestine
38	chr2:40471000-40471600	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr2:40471000-40471800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:40471000-40472000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:40471000-40472000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr2:40471000-40472000	Enhancers	Right Ventricle	heart
43	chr2:40471000-40472400	Enhancers	Adipose Nuclei	Adipose
44	chr2:40471000-40472800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr2:40471200-40471600	Enhancers	Colonic Mucosa	Colon
46	chr2:40471200-40471600	Flanking Active TSS	Osteobl	bone
47	chr2:40471200-40471800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:40471200-40472000	Enhancers	Duodenum Mucosa	Duodenum
49	chr2:40471200-40472200	Enhancers	Psoas Muscle	Psoas
50	chr2:40471200-40472200	Enhancers	Stomach Mucosa	stomach

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