Variant report

Variant	rs10490208
Chromosome Location	chr2:40453794-40453795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11124737	0.82[CHD][hapmap]
rs11674102	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs11682111	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682470	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11690292	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11691096	0.91[AMR][1000 genomes]
rs12104840	0.80[CEU][hapmap];0.93[CHB][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs12474968	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13394655	0.88[CEU][hapmap]
rs1428579	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17503184	0.83[MEX][hapmap]
rs17504446	0.82[ASW][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes]
rs17504670	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1985526	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35113834	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4581943	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs4952401	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4952591	0.83[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs4952594	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952599	0.87[CHB][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap]
rs6736607	0.94[ASN][1000 genomes]
rs7558668	0.88[CEU][hapmap]
rs7558770	0.83[MEX][hapmap]
rs7558787	0.83[MEX][hapmap]
rs7588446	0.94[ASN][1000 genomes]
rs7593406	0.90[CHD][hapmap];0.80[GIH][hapmap]
rs7602176	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap]
rs877099	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs918050	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873910	chr2:40391907-40466268	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv524586	chr2:40447587-40497501	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40446400-40454400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:40446400-40455400	Weak transcription	Psoas Muscle	Psoas
3	chr2:40447800-40454400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:40447800-40457600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:40448000-40487400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:40448200-40455400	Weak transcription	HSMM	muscle
7	chr2:40451200-40454200	Weak transcription	Osteobl	bone
8	chr2:40451400-40455600	Weak transcription	Aorta	Aorta
9	chr2:40451400-40490000	Weak transcription	Dnd41	blood
10	chr2:40452000-40454600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:40452200-40453800	Enhancers	Rectal Smooth Muscle	rectum
12	chr2:40452200-40454000	Enhancers	Fetal Brain Male	brain
13	chr2:40452200-40454000	Enhancers	Fetal Brain Female	brain
14	chr2:40452400-40454400	Enhancers	Fetal Heart	heart
15	chr2:40452400-40454800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:40452600-40453800	Enhancers	Fetal Muscle Leg	muscle
17	chr2:40452600-40453800	Enhancers	Fetal Stomach	stomach
18	chr2:40452600-40454200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:40452600-40454200	Enhancers	Stomach Smooth Muscle	stomach
20	chr2:40452600-40454600	Enhancers	Colon Smooth Muscle	Colon
21	chr2:40452600-40455600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr2:40452800-40454000	Enhancers	Brain Germinal Matrix	brain
23	chr2:40453000-40453800	Enhancers	H9 Cell Line	embryonic stem cell
24	chr2:40453000-40453800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:40453200-40453800	Enhancers	Right Ventricle	heart
26	chr2:40453400-40453800	Enhancers	Right Atrium	heart
27	chr2:40453400-40454400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:40453600-40454400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:40453600-40454400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:40453600-40454800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:40453600-40455400	Weak transcription	Left Ventricle	heart
32	chr2:40453600-40455400	Weak transcription	HSMMtube	muscle
33	chr2:40453600-40455600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr2:40453600-40455800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:40453600-40457200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:40453600-40457200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:40453600-40459400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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