Variant report

Variant	rs469994
Chromosome Location	chr22:29401333-29401334
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12484832	0.96[CEU][hapmap]
rs132565	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17440734	1.00[CEU][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes]
rs1983553	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2064084	0.96[CEU][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2072774	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2347789	0.82[EUR][1000 genomes]
rs2347790	0.92[CEU][hapmap]
rs28541979	0.88[ASN][1000 genomes]
rs4140643	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4333023	0.82[EUR][1000 genomes]
rs4404379	0.81[EUR][1000 genomes]
rs4580479	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4820794	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4823002	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4823003	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4823005	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997430	0.81[EUR][1000 genomes]
rs5997432	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5997433	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs5997435	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6005954	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005955	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs6005956	0.93[CEU][hapmap]
rs6005958	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs6005964	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6005965	1.00[CEU][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs6005967	0.96[CEU][hapmap]
rs713834	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs727892	1.00[CEU][hapmap]
rs7290304	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs738246	0.96[CEU][hapmap]
rs8137254	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs8137499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874916	0.80[EUR][1000 genomes]
rs874917	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9608719	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9608721	0.88[ASN][1000 genomes]
rs9613771	0.81[EUR][1000 genomes]
rs9613776	0.93[CEU][hapmap]
rs9613777	0.92[CEU][hapmap]
rs9613784	0.88[ASN][1000 genomes]
rs9613785	0.96[CEU][hapmap]
rs964589	0.96[CEU][hapmap]

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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29396000-29401400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr22:29397800-29402200	Enhancers	Fetal Heart	heart
3	chr22:29398000-29402000	Enhancers	Fetal Muscle Leg	muscle
4	chr22:29398600-29402600	Enhancers	Pancreas	Pancrea
5	chr22:29398800-29405000	Weak transcription	HSMMtube	muscle
6	chr22:29399400-29402000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr22:29399400-29403200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr22:29399600-29401400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr22:29399600-29401800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr22:29399600-29401800	Enhancers	Brain Cingulate Gyrus	brain
11	chr22:29399600-29403400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr22:29399800-29401400	Enhancers	Fetal Muscle Trunk	muscle
13	chr22:29399800-29401400	Enhancers	HMEC	breast
14	chr22:29400000-29401400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr22:29400000-29401400	Weak transcription	Brain Angular Gyrus	brain
16	chr22:29400000-29401400	Enhancers	Small Intestine	intestine
17	chr22:29400000-29401600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr22:29400000-29401600	Enhancers	H9 Cell Line	embryonic stem cell
19	chr22:29400000-29401600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:29400000-29401600	Enhancers	Brain Hippocampus Middle	brain
21	chr22:29400000-29401600	Enhancers	Fetal Kidney	kidney
22	chr22:29400000-29401800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr22:29400000-29401800	Enhancers	Liver	Liver
24	chr22:29400000-29401800	Enhancers	Brain Anterior Caudate	brain
25	chr22:29400000-29401800	Bivalent Enhancer	Fetal Thymus	thymus
26	chr22:29400000-29401800	Enhancers	Left Ventricle	heart
27	chr22:29400000-29401800	Enhancers	Right Ventricle	heart
28	chr22:29400000-29401800	Flanking Active TSS	HepG2	liver
29	chr22:29400000-29402000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr22:29400200-29401400	Enhancers	Right Atrium	heart
31	chr22:29400200-29401600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr22:29400200-29401600	Enhancers	Brain Germinal Matrix	brain
33	chr22:29400200-29401800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr22:29400200-29401800	Enhancers	Fetal Lung	lung
35	chr22:29400400-29401400	Enhancers	Primary hematopoietic stem cells	blood
36	chr22:29400400-29401400	Enhancers	Ovary	ovary
37	chr22:29400400-29401400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr22:29400400-29401400	Enhancers	NH-A	brain
39	chr22:29400400-29401600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr22:29400400-29401600	Enhancers	Psoas Muscle	Psoas
41	chr22:29400400-29401800	Enhancers	Lung	lung
42	chr22:29400400-29402200	Enhancers	Placenta	Placenta
43	chr22:29400600-29401400	Weak transcription	Brain Substantia Nigra	brain
44	chr22:29400600-29401400	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr22:29400600-29412000	Weak transcription	A549	lung
46	chr22:29400600-29425400	Weak transcription	NHEK	skin
47	chr22:29400800-29401400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr22:29400800-29401400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr22:29400800-29401400	Enhancers	Esophagus	oesophagus
50	chr22:29400800-29401600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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