Variant report

Variant	rs11890896
Chromosome Location	chr2:55436996-55436997
allele	A/G
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	GATA3	chr2:55436529-55437030	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55435664..55437797-chr2:55450159..55452087,2	MCF-7	breast:

Variant related genes	Relation type
CLHC1	TF binding region
ENSG00000162994	Chromatin interaction
ENSG00000227799	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10172326	0.88[YRI][hapmap]
rs10209298	1.00[EUR][1000 genomes]
rs11679663	0.96[YRI][hapmap]
rs11886358	1.00[EUR][1000 genomes]
rs11887112	1.00[EUR][1000 genomes]
rs11888119	1.00[MEX][hapmap]
rs11889466	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11894557	1.00[MEX][hapmap]
rs11896438	1.00[EUR][1000 genomes]
rs11899921	1.00[MEX][hapmap]
rs11902622	1.00[EUR][1000 genomes]
rs12621144	0.92[YRI][hapmap]
rs13012766	0.96[YRI][hapmap]
rs13013134	0.96[YRI][hapmap]
rs13019355	1.00[YRI][hapmap]
rs13399572	1.00[MEX][hapmap]
rs17046771	1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046787	0.85[ASW][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes]
rs2972077	1.00[EUR][1000 genomes]
rs3935223	0.88[YRI][hapmap]
rs55726603	0.91[AMR][1000 genomes]
rs55735105	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56219595	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56887573	0.91[AMR][1000 genomes]
rs56902676	0.91[AMR][1000 genomes]
rs57489147	0.91[AMR][1000 genomes]
rs57517202	0.91[AMR][1000 genomes]
rs58016152	1.00[EUR][1000 genomes]
rs58207828	0.91[AMR][1000 genomes]
rs58485503	0.91[AMR][1000 genomes]
rs60944260	1.00[EUR][1000 genomes]
rs61197615	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545474	0.92[YRI][hapmap]
rs6545478	0.96[YRI][hapmap]
rs6707902	1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6714830	0.92[YRI][hapmap]
rs6716121	1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6721728	1.00[MEX][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes]
rs6723598	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6724153	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6736539	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73936831	1.00[EUR][1000 genomes]
rs73936834	1.00[EUR][1000 genomes]
rs73936837	1.00[EUR][1000 genomes]
rs73936845	1.00[EUR][1000 genomes]
rs73936947	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73936949	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73936959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73936964	0.91[AMR][1000 genomes]
rs7596403	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7608709	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers 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	25 gene(s)	inside rSNPs	diseases
3	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55397200-55450000	Weak transcription	NH-A	brain
2	chr2:55402800-55450000	Weak transcription	NHDF-Ad	bronchial
3	chr2:55415400-55450000	Weak transcription	GM12878-XiMat	blood
4	chr2:55416800-55450000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:55417400-55450200	Weak transcription	Placenta	Placenta
6	chr2:55417800-55439200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:55417800-55450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:55423200-55438800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:55423800-55448000	Weak transcription	HSMM	muscle
10	chr2:55424200-55450000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:55424400-55442200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:55424600-55442800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:55424600-55449800	Weak transcription	Thymus	Thymus
14	chr2:55424600-55450000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:55424600-55450200	Weak transcription	Brain Germinal Matrix	brain
16	chr2:55424600-55451200	Weak transcription	HepG2	liver
17	chr2:55424800-55450200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:55425600-55449800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:55427400-55450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:55427400-55450200	Weak transcription	Aorta	Aorta
21	chr2:55427400-55450600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:55427400-55450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:55428800-55439400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:55429200-55449800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:55430000-55437800	Weak transcription	Fetal Intestine Large	intestine
26	chr2:55430000-55443200	Weak transcription	Fetal Intestine Small	intestine
27	chr2:55430000-55450400	Weak transcription	Left Ventricle	heart
28	chr2:55431000-55439400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:55432000-55449800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:55432000-55451200	Weak transcription	Dnd41	blood
31	chr2:55432200-55450000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:55432600-55448800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:55432800-55450000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:55432800-55450000	Weak transcription	Fetal Stomach	stomach
35	chr2:55433000-55444600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:55433000-55448800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:55433000-55448800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:55433000-55449800	Weak transcription	Pancreas	Pancrea
39	chr2:55433000-55450200	Weak transcription	Ovary	ovary
40	chr2:55433400-55450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:55433600-55448200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:55433600-55448600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:55435200-55437000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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