Variant report

Variant	rs16871220
Chromosome Location	chr5:41335118-41335119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10462017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10512774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10512775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11737958	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11739235	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11739338	0.84[ASN][1000 genomes]
rs11739372	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11739553	1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs11739969	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11740787	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11741144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11744499	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11747859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1373639	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1423312	0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs1460953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161086	0.82[CEU][hapmap]
rs1645060	0.82[CEU][hapmap]
rs167628	0.82[CEU][hapmap]
rs16871219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16871222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16871258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16871269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1822820	1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs1904178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1904179	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2054445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2197422	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs223080	0.82[CEU][hapmap]
rs2329601	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2860000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2925729	0.82[CEU][hapmap]
rs2925731	0.82[CEU][hapmap]
rs318844	0.82[CEU][hapmap]
rs320623	0.82[CEU][hapmap]
rs4245978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4403222	0.82[CEU][hapmap]
rs4557464	0.82[CEU][hapmap]
rs4957153	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]
rs4957389	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4957390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4957391	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957392	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60271243	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60917374	0.97[ASN][1000 genomes]
rs61282403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67043243	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6859578	0.82[CEU][hapmap]
rs6872806	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6886372	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6886899	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6898606	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs72755961	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72755967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72755968	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72755970	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72755972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72755973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72755982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72755983	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72755984	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73075962	0.88[ASN][1000 genomes]
rs765176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701760	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7703589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722338	0.82[CEU][hapmap]
rs7723649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724627	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7725517	0.96[ASN][1000 genomes]
rs7727658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7729454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7735604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs978727	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427717	chr5:41201377-41369202	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv830269	chr5:41209113-41393536	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41329400-41335200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:41333400-41337200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:41333600-41336000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:41333800-41336000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr5:41333800-41345800	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr5:41334000-41335800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr5:41334000-41336600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:41334000-41337600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:41334200-41335400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:41334200-41335400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr5:41334200-41335400	Enhancers	Fetal Lung	lung
12	chr5:41334200-41335600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr5:41334200-41336000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:41334200-41336200	Enhancers	Fetal Heart	heart
15	chr5:41334400-41335200	Weak transcription	Colon Smooth Muscle	Colon
16	chr5:41334400-41335400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:41334400-41335400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr5:41334400-41335400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:41334400-41335400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:41334400-41335400	Enhancers	Left Ventricle	heart
21	chr5:41334400-41335600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:41334400-41335600	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr5:41334400-41335600	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr5:41334400-41335600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr5:41334400-41335800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr5:41334600-41335200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:41334600-41335200	Active TSS	Brain Anterior Caudate	brain
28	chr5:41334600-41335400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:41334600-41335600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:41334600-41335600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr5:41334600-41335800	Weak transcription	Right Ventricle	heart
32	chr5:41334800-41335200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:41334800-41335200	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr5:41334800-41336200	Weak transcription	Adipose Nuclei	Adipose
35	chr5:41334800-41336200	Enhancers	Brain Cingulate Gyrus	brain
36	chr5:41334800-41336200	Enhancers	Ovary	ovary
37	chr5:41335000-41335400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr5:41335000-41335400	Enhancers	A549	lung
39	chr5:41335000-41336800	Enhancers	Brain Substantia Nigra	brain
40	chr5:41335000-41336800	Weak transcription	Right Atrium	heart

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