Variant report

Variant	rs17049417
Chromosome Location	chr2:58441542-58441543
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10188390	0.85[CEU][hapmap]
rs10496086	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10496087	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs11898024	0.85[CEU][hapmap];0.95[TSI][hapmap]
rs12470851	0.85[CEU][hapmap];0.95[TSI][hapmap]
rs12471043	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs12473840	0.85[CEU][hapmap]
rs12474593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12475192	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs12476829	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12478718	0.85[CEU][hapmap]
rs1371212	0.85[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs1518403	0.85[CEU][hapmap]
rs17049312	0.85[CEU][hapmap]
rs17049314	0.85[CEU][hapmap];0.95[TSI][hapmap]
rs17049316	0.85[CEU][hapmap]
rs17049394	0.85[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17049416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049423	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17326957	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17830749	0.85[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs2118897	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2192689	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs36000054	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56028716	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72810350	0.85[EUR][1000 genomes]
rs72810351	0.85[EUR][1000 genomes]
rs72810352	0.85[EUR][1000 genomes]
rs72810385	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72810394	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72812352	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs728574	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv458052	chr2:58388696-58450569	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv582098	chr2:58388696-58450569	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv817995	chr2:58390538-58450569	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:58391000-58467000	Weak transcription	HMEC	breast
3	chr2:58397800-58442600	Weak transcription	Brain Anterior Caudate	brain
4	chr2:58414000-58461400	Weak transcription	NHEK	skin
5	chr2:58416200-58454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:58416600-58467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:58421600-58452400	Weak transcription	NH-A	brain
8	chr2:58422000-58442800	Weak transcription	Brain Angular Gyrus	brain
9	chr2:58422000-58454200	Weak transcription	Left Ventricle	heart
10	chr2:58425000-58442200	Weak transcription	Fetal Heart	heart
11	chr2:58425600-58446600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:58425800-58446600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:58432000-58445600	Weak transcription	Osteobl	bone
14	chr2:58432000-58466400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:58432200-58442400	Weak transcription	HUVEC	blood vessel
16	chr2:58433600-58454200	Weak transcription	Gastric	stomach
17	chr2:58437000-58460200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:58437200-58442400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:58437200-58442800	ZNF genes & repeats	GM12878-XiMat	blood
20	chr2:58437200-58459000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:58437400-58441600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:58437600-58443200	Weak transcription	Right Atrium	heart
23	chr2:58437800-58456800	Weak transcription	Fetal Kidney	kidney
24	chr2:58438600-58442000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:58438600-58442000	Weak transcription	Ovary	ovary
26	chr2:58438600-58442200	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:58438600-58442400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:58438600-58442600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:58438600-58442600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:58438600-58443000	Weak transcription	Brain Germinal Matrix	brain
31	chr2:58438600-58443800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:58438600-58443800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr2:58438600-58444000	Strong transcription	A549	lung
34	chr2:58438600-58454200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:58438600-58454200	Weak transcription	Aorta	Aorta
36	chr2:58438600-58454200	Weak transcription	Esophagus	oesophagus
37	chr2:58438600-58454200	Weak transcription	Fetal Brain Female	brain
38	chr2:58438600-58454200	Weak transcription	Fetal Stomach	stomach
39	chr2:58438600-58454200	Weak transcription	Lung	lung
40	chr2:58438600-58454200	Weak transcription	Pancreas	Pancrea
41	chr2:58438600-58454200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:58438600-58454200	Weak transcription	Thymus	Thymus
43	chr2:58438600-58466400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:58438800-58441600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:58438800-58454200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:58438800-58454200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:58439000-58446600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:58439000-58467400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:58439200-58442600	Weak transcription	Brain Substantia Nigra	brain
50	chr2:58439200-58454200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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