Variant report

Variant	rs12562335
Chromosome Location	chr1:77644415-77644416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10443176	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11162275	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11162284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11162287	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12077763	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12090495	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12119019	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12120921	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12122553	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12123535	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12126662	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12143529	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1502525	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17368950	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1827448	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4949772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4949773	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4949778	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61782906	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6603937	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6696605	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7519485	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7544099	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7550325	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][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	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77606200-77651600	Weak transcription	Aorta	Aorta
2	chr1:77616200-77663200	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:77626000-77662600	Weak transcription	Thymus	Thymus
4	chr1:77626000-77684200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:77626800-77668000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:77626800-77674800	Weak transcription	Ovary	ovary
7	chr1:77626800-77676200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:77630800-77652000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:77630800-77660600	Weak transcription	Left Ventricle	heart
10	chr1:77631800-77660600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:77634400-77656600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:77637800-77647800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:77638200-77662200	Weak transcription	Small Intestine	intestine
14	chr1:77639400-77645800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr1:77642400-77645200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:77642800-77646400	Weak transcription	Fetal Heart	heart
17	chr1:77643400-77649800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:77643400-77669600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:77643600-77645200	ZNF genes & repeats	Primary T cells from cord blood	blood
20	chr1:77643600-77663000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:77643600-77672600	Weak transcription	Fetal Lung	lung
22	chr1:77643800-77674400	Weak transcription	Psoas Muscle	Psoas
23	chr1:77644000-77644600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:77644000-77654800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:77644200-77652000	Weak transcription	Primary B cells from cord blood	blood

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