Variant report

Variant	rs1437392
Chromosome Location	chr2:55445518-55445519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55445506-55445578	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55444067..55446129-chr2:55459574..55462143,2	MCF-7	breast:
2	chr2:55439611..55442665-chr2:55443845..55449055,6	K562	blood:
3	chr2:55439611..55442389-chr2:55444067..55447159,3	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTIF2-3	chr2:55445481-55445736	NONHSAT070768
2	lnc-MTIF2-3	chr2:55445256-55445736	NONHSAT070767

No data

Variant related genes	Relation type
ENSG00000203327	TF binding region
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10176839	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10183953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191785	1.00[CEU][hapmap]
rs10439479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892007	0.82[JPT][hapmap]
rs11904107	0.82[JPT][hapmap]
rs12104902	0.82[JPT][hapmap]
rs12105731	0.82[JPT][hapmap]
rs12464094	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12617316	0.82[JPT][hapmap]
rs12713290	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002841	0.82[JPT][hapmap]
rs13031346	0.82[JPT][hapmap]
rs1437387	0.82[JPT][hapmap]
rs1437388	0.82[JPT][hapmap]
rs1437389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561231	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561232	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1561233	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17046834	0.82[JPT][hapmap]
rs17046915	1.00[CEU][hapmap]
rs2028138	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2043714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164715	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249856	0.82[JPT][hapmap]
rs2289168	0.82[JPT][hapmap]
rs2576692	0.82[JPT][hapmap]
rs2576693	0.82[JPT][hapmap]
rs2576699	0.82[JPT][hapmap]
rs2576702	0.82[JPT][hapmap]
rs2576723	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589060	0.82[JPT][hapmap]
rs2589061	0.82[JPT][hapmap]
rs2589063	0.82[JPT][hapmap]
rs2589081	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589082	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589083	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2589097	0.87[EUR][1000 genomes]
rs2589098	0.87[EUR][1000 genomes]
rs2589111	0.82[JPT][hapmap]
rs2589113	0.82[JPT][hapmap]
rs2920845	0.86[EUR][1000 genomes]
rs2920846	0.83[EUR][1000 genomes]
rs2920869	0.86[EUR][1000 genomes]
rs2966465	0.82[JPT][hapmap]
rs2968816	0.82[JPT][hapmap]
rs2968820	0.82[JPT][hapmap]
rs2972087	0.82[JPT][hapmap]
rs3929128	0.82[AFR][1000 genomes]
rs4233959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4591380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57885021	0.90[AFR][1000 genomes]
rs6545476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545482	0.82[JPT][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes]
rs6545484	0.82[JPT][hapmap]
rs6713058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718747	0.82[JPT][hapmap]
rs6719579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726732	0.82[JPT][hapmap]
rs6733567	0.82[JPT][hapmap]
rs6746287	0.82[JPT][hapmap]
rs6746757	1.00[CEU][hapmap]
rs6746983	1.00[CEU][hapmap]
rs6747682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747974	1.00[CEU][hapmap]
rs6750501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754605	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6759310	1.00[CEU][hapmap]
rs6759957	1.00[CEU][hapmap]
rs9784090	0.82[JPT][hapmap]

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:39 , 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	chr2:55417800-55450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:55423800-55448000	Weak transcription	HSMM	muscle
8	chr2:55424200-55450000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:55424600-55449800	Weak transcription	Thymus	Thymus
10	chr2:55424600-55450000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:55424600-55450200	Weak transcription	Brain Germinal Matrix	brain
12	chr2:55424600-55451200	Weak transcription	HepG2	liver
13	chr2:55424800-55450200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:55425600-55449800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:55427400-55450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:55427400-55450200	Weak transcription	Aorta	Aorta
17	chr2:55427400-55450600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:55427400-55450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:55429200-55449800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:55430000-55450400	Weak transcription	Left Ventricle	heart
21	chr2:55432000-55449800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:55432000-55451200	Weak transcription	Dnd41	blood
23	chr2:55432200-55450000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:55432600-55448800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:55432800-55450000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:55432800-55450000	Weak transcription	Fetal Stomach	stomach
27	chr2:55433000-55448800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:55433000-55448800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:55433000-55449800	Weak transcription	Pancreas	Pancrea
30	chr2:55433000-55450200	Weak transcription	Ovary	ovary
31	chr2:55433400-55450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:55433600-55448200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:55433600-55448600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:55441200-55450000	Weak transcription	K562	blood
35	chr2:55441400-55450000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:55442800-55446800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:55444400-55450400	Weak transcription	Gastric	stomach
38	chr2:55444600-55449800	Weak transcription	Fetal Intestine Small	intestine
39	chr2:55445200-55448800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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