Variant report

Variant	rs11125096
Chromosome Location	chr2:47083655-47083656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:47081386-47084203	A549	lung:	n/a	chr2:47083633-47083643 chr2:47083889-47083899 chr2:47082487-47082496 chr2:47082537-47082546 chr2:47082693-47082703 chr2:47082538-47082547
2	JUND	chr2:47081996-47083816	SK-N-SH	brain:	n/a	chr2:47082538-47082546 chr2:47082538-47082545 chr2:47082537-47082547 chr2:47082536-47082548 chr2:47082487-47082495 chr2:47082486-47082496 chr2:47082537-47082546 chr2:47082487-47082495 chr2:47082485-47082497 chr2:47082536-47082547 chr2:47082487-47082494
3	TCF12	chr2:47081827-47083769	A549	lung:	n/a	chr2:47082192-47082202 chr2:47082699-47082709

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46926240..46928505-chr2:47083626..47085275,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226548	TF binding region
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10170987	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10177555	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10177751	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10183609	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11125097	0.87[ASN][1000 genomes]
rs11687883	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11689551	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2166478	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278711	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278712	0.81[ASN][1000 genomes]
rs34392693	0.81[ASN][1000 genomes]
rs4953433	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6759066	0.81[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9225	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935372	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs935379	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47075200-47084400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:47077200-47086200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:47078000-47085200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:47078000-47085200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:47080600-47085000	Weak transcription	K562	blood
6	chr2:47080800-47084200	Enhancers	Left Ventricle	heart
7	chr2:47080800-47103600	Enhancers	Placenta	Placenta
8	chr2:47081200-47083800	Enhancers	Rectal Smooth Muscle	rectum
9	chr2:47081200-47087200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:47081400-47083800	Enhancers	Colon Smooth Muscle	Colon
11	chr2:47081400-47083800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr2:47081400-47083800	Enhancers	HSMMtube	muscle
13	chr2:47081400-47084000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:47081400-47086400	Enhancers	HMEC	breast
15	chr2:47081400-47086600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:47081400-47087200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr2:47081400-47087800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:47081400-47091000	Enhancers	NHDF-Ad	bronchial
19	chr2:47081600-47084000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:47081600-47084000	Enhancers	Ovary	ovary
21	chr2:47081600-47084000	Enhancers	Right Atrium	heart
22	chr2:47081600-47084200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:47081600-47084200	Enhancers	Esophagus	oesophagus
24	chr2:47081600-47084200	Enhancers	Lung	lung
25	chr2:47081600-47084400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:47081600-47084400	Enhancers	HSMM	muscle
27	chr2:47081600-47085600	Enhancers	NH-A	brain
28	chr2:47081600-47087800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr2:47082200-47084000	Flanking Active TSS	Hela-S3	cervix
30	chr2:47082200-47085000	Weak transcription	Small Intestine	intestine
31	chr2:47082200-47085200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:47082200-47085200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:47082200-47085400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:47082200-47089000	Weak transcription	Colonic Mucosa	Colon
35	chr2:47082600-47083800	Enhancers	Fetal Intestine Small	intestine
36	chr2:47082800-47084400	Enhancers	Stomach Smooth Muscle	stomach
37	chr2:47082800-47085000	Weak transcription	Fetal Lung	lung
38	chr2:47083000-47084000	Enhancers	HUVEC	blood vessel
39	chr2:47083000-47084400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:47083000-47086200	Weak transcription	Adipose Nuclei	Adipose
41	chr2:47083200-47083800	Flanking Active TSS	A549	lung
42	chr2:47083200-47084000	Enhancers	Pancreas	Pancrea
43	chr2:47083200-47084000	Enhancers	Psoas Muscle	Psoas
44	chr2:47083200-47084000	Enhancers	Right Ventricle	heart
45	chr2:47083200-47088600	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:47083400-47084000	Genic enhancers	NHLF	lung
47	chr2:47083400-47084200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:47083400-47084200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:47083400-47084400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr2:47083400-47085000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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