Variant report

Variant	rs3816729
Chromosome Location	chr5:80040532-80040533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1428030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1805355	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs181747	0.85[ASN][1000 genomes]
rs2195291	0.82[CEU][hapmap]
rs3776969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776970	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3776971	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3797877	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3797885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797896	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4703818	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4704680	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4704681	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4704683	0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6151628	0.82[CEU][hapmap]
rs6151639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];1.00[TSI][hapmap]
rs6151685	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151705	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151714	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151769	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151789	0.89[AMR][1000 genomes]
rs6151826	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6151865	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6879843	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6881898	0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6894961	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs73125417	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7711890	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7721000	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs836812	0.81[JPT][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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv882231	chr5:79984714-80187929	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv3421113	chr5:80038646-80040644	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
4	chr5:79998600-80051000	Weak transcription	Fetal Brain Male	brain
5	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:80004000-80050400	Weak transcription	NHDF-Ad	bronchial
7	chr5:80016000-80040600	Weak transcription	Small Intestine	intestine
8	chr5:80016200-80040600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:80016200-80040600	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:80016200-80043600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:80016400-80050800	Weak transcription	Psoas Muscle	Psoas
12	chr5:80020200-80043600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:80022800-80040600	Weak transcription	Spleen	Spleen
14	chr5:80022800-80041400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:80022800-80051200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:80023000-80040600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:80023000-80040600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:80023000-80040600	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:80023000-80040600	Weak transcription	HUVEC	blood vessel
20	chr5:80023000-80041400	Weak transcription	Fetal Brain Female	brain
21	chr5:80023000-80043000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:80023000-80043200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:80024000-80041400	Weak transcription	NH-A	brain
24	chr5:80024200-80040600	Weak transcription	Brain Anterior Caudate	brain
25	chr5:80024200-80040600	Weak transcription	Brain Substantia Nigra	brain
26	chr5:80024200-80046800	Weak transcription	Brain Angular Gyrus	brain
27	chr5:80024400-80043400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr5:80026000-80042000	Weak transcription	GM12878-XiMat	blood
29	chr5:80026200-80040600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr5:80032400-80045400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr5:80032800-80043600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr5:80033200-80051400	Weak transcription	HMEC	breast
33	chr5:80034200-80049400	Strong transcription	Primary T cells from cord blood	blood
34	chr5:80034800-80050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr5:80035000-80050400	Weak transcription	Stomach Mucosa	stomach
36	chr5:80035200-80042200	Weak transcription	HSMMtube	muscle
37	chr5:80036200-80041400	Weak transcription	NHLF	lung
38	chr5:80036400-80043800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr5:80037000-80042400	Strong transcription	Fetal Thymus	thymus
40	chr5:80037200-80040800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:80037200-80049800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:80037200-80050600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr5:80037400-80042400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:80037400-80045800	Strong transcription	Liver	Liver
45	chr5:80037400-80049000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:80037400-80050600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr5:80037600-80040600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:80037600-80044000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr5:80037600-80049000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:80037600-80050200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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