Variant report

Variant	rs6005779
Chromosome Location	chr22:28807277-28807278
allele	C/T
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:37)

rs_ID	r²[population]
rs12157518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12159502	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs16986103	0.84[ASN][1000 genomes]
rs16986290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.88[ASN][1000 genomes]
rs16986377	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16986462	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16986548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35731009	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58427200	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997341	0.84[ASN][1000 genomes]
rs5997355	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs5997363	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5997365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997372	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005724	0.82[ASN][1000 genomes]
rs6005726	0.84[ASN][1000 genomes]
rs6005733	0.88[ASN][1000 genomes]
rs6005735	0.88[ASN][1000 genomes]
rs6005751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6005757	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6005758	0.93[ASN][1000 genomes]
rs6005765	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005780	0.97[EUR][1000 genomes]
rs6005783	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6005789	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005793	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005829	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6005833	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6005834	0.85[EUR][1000 genomes]
rs73427747	0.88[ASN][1000 genomes]
rs73428082	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73428096	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73430108	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs738199	0.87[YRI][hapmap]
rs7510988	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv588880	chr22:28807277-29001789	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28793000-28808200	Weak transcription	Aorta	Aorta
2	chr22:28793000-28808600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr22:28793000-28814000	Weak transcription	Left Ventricle	heart
4	chr22:28793000-28819800	Weak transcription	Fetal Intestine Small	intestine
5	chr22:28798400-28809800	Weak transcription	Fetal Lung	lung
6	chr22:28798800-28821200	Weak transcription	Dnd41	blood
7	chr22:28801000-28810000	Weak transcription	Fetal Kidney	kidney
8	chr22:28803800-28807600	Weak transcription	Fetal Brain Female	brain
9	chr22:28804600-28810000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:28805000-28808200	Weak transcription	Ovary	ovary
11	chr22:28805200-28809600	Weak transcription	Fetal Stomach	stomach
12	chr22:28805200-28810400	Weak transcription	Fetal Brain Male	brain
13	chr22:28805400-28807400	Weak transcription	Brain Angular Gyrus	brain
14	chr22:28805400-28807600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr22:28805400-28807600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr22:28805800-28808000	Weak transcription	Psoas Muscle	Psoas
17	chr22:28805800-28808800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr22:28806000-28807600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr22:28806000-28808000	Enhancers	Osteobl	bone
20	chr22:28806200-28807800	Enhancers	Rectal Smooth Muscle	rectum
21	chr22:28806200-28813000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr22:28806400-28807400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr22:28806600-28807400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr22:28806600-28807400	Weak transcription	Brain Hippocampus Middle	brain
25	chr22:28806600-28807600	Enhancers	NHDF-Ad	bronchial
26	chr22:28806600-28808200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr22:28806600-28809800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr22:28806600-28809800	Weak transcription	HSMMtube	muscle
29	chr22:28806600-28810000	Weak transcription	NHLF	lung
30	chr22:28806800-28807400	Weak transcription	Brain Germinal Matrix	brain
31	chr22:28806800-28807600	Weak transcription	Brain Anterior Caudate	brain
32	chr22:28806800-28807800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr22:28806800-28808000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr22:28806800-28808200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr22:28806800-28809800	Weak transcription	Brain Substantia Nigra	brain
36	chr22:28806800-28809800	Weak transcription	HUVEC	blood vessel
37	chr22:28806800-28810000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr22:28806800-28815400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr22:28806800-28815800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr22:28807000-28807800	Enhancers	Colon Smooth Muscle	Colon
41	chr22:28807200-28807400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr22:28807200-28807800	Enhancers	Adipose Nuclei	Adipose
43	chr22:28807200-28808600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr22:28807200-28809800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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