Variant report

Variant	rs13419989
Chromosome Location	chr2:58290441-58290442
allele	C/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	POLR2A	chr2:58290404-58290642	GM12878	blood:	n/a	n/a
2	STAT3	chr2:58290420-58290683	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:58288671-58291267	K562	blood:	n/a	n/a
4	POLR2A	chr2:58290396-58290446	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000251738	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10165760	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10174202	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10176681	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10176942	0.89[AMR][1000 genomes]
rs10178025	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10182762	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10187411	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10203014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1025755	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11883874	0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11891477	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11892302	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13382369	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13394820	0.98[AFR][1000 genomes]
rs13405281	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13410500	0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13431271	0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1371213	0.89[AMR][1000 genomes]
rs2165100	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2165103	0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2312486	0.89[AMR][1000 genomes]
rs28521626	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4459722	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57112138	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs57597086	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58470176	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs60364084	0.89[AMR][1000 genomes]
rs6718190	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs716758	0.89[AMR][1000 genomes]
rs72949131	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72949137	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72949158	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72951042	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72951048	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72951056	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73944804	0.89[AFR][1000 genomes]
rs7563312	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7569731	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7574578	0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7574694	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7600213	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9973345	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9973928	0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv582097	chr2:58266099-58346966	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv874201	chr2:58269871-58350504	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv874202	chr2:58269871-58375688	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58274600-58298600	Weak transcription	Spleen	Spleen
2	chr2:58274600-58302400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:58274800-58296400	Weak transcription	Ovary	ovary
4	chr2:58274800-58296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:58274800-58302200	Weak transcription	Aorta	Aorta
6	chr2:58274800-58317400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:58275000-58290800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:58275000-58290800	Weak transcription	Thymus	Thymus
9	chr2:58275000-58291000	Weak transcription	HSMM	muscle
10	chr2:58275000-58297600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:58275000-58302600	Weak transcription	Esophagus	oesophagus
12	chr2:58275000-58302800	Weak transcription	Fetal Stomach	stomach
13	chr2:58275000-58305600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:58275000-58317400	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:58275000-58321600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:58275000-58326600	Weak transcription	Pancreas	Pancrea
17	chr2:58275400-58290600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:58275400-58290600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:58275400-58290800	Weak transcription	Brain Anterior Caudate	brain
20	chr2:58275400-58291000	Weak transcription	NH-A	brain
21	chr2:58275400-58294400	Weak transcription	Fetal Intestine Small	intestine
22	chr2:58275600-58291000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:58275600-58291000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:58275600-58293800	Weak transcription	Small Intestine	intestine
25	chr2:58275800-58290600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:58275800-58316800	Weak transcription	HMEC	breast
27	chr2:58276800-58290600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:58279000-58319000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:58279400-58315600	Weak transcription	Dnd41	blood
30	chr2:58281000-58297800	Weak transcription	Fetal Lung	lung
31	chr2:58282200-58291400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr2:58282400-58291000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:58282400-58300400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:58282400-58301400	Weak transcription	Lung	lung
35	chr2:58282600-58350400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:58283200-58290600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:58283400-58294400	Strong transcription	Primary B cells from cord blood	blood
38	chr2:58283400-58296600	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:58283600-58298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:58284200-58295400	Weak transcription	Psoas Muscle	Psoas
41	chr2:58284200-58296400	Weak transcription	Left Ventricle	heart
42	chr2:58284200-58303800	Weak transcription	Gastric	stomach
43	chr2:58284200-58317600	Weak transcription	HepG2	liver
44	chr2:58284400-58325000	Weak transcription	NHEK	skin
45	chr2:58284800-58291600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr2:58285200-58291000	Weak transcription	Right Ventricle	heart
47	chr2:58285200-58317000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr2:58285800-58293200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:58286000-58290600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:58286000-58296400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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