Variant report

Variant	rs3772504
Chromosome Location	chr3:59980746-59980747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12497400	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17031569	1.00[JPT][hapmap]
rs17061546	1.00[JPT][hapmap]
rs17061598	1.00[JPT][hapmap]
rs17061678	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17061689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17061708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17254574	0.86[EUR][1000 genomes]
rs17255191	0.82[EUR][1000 genomes]
rs3772474	1.00[JPT][hapmap]
rs3772487	1.00[JPT][hapmap]
rs3772489	1.00[JPT][hapmap]
rs3772503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3821484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs58024458	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62238369	0.84[EUR][1000 genomes]
rs62238370	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62238371	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72877063	0.81[EUR][1000 genomes]
rs7626013	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv876838	chr3:59952152-59999690	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv590388	chr3:59957252-60018326	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59967400-59993000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:59968000-59986600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:59968400-59982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:59972800-59983600	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr3:59974200-59983000	Enhancers	Fetal Thymus	thymus
6	chr3:59974400-59983000	Enhancers	Thymus	Thymus
7	chr3:59975200-59984000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:59976000-59981000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:59976800-59984000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:59977000-59981600	Strong transcription	Dnd41	blood
11	chr3:59977200-59983800	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr3:59978200-59985000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:59978400-59984600	Enhancers	Primary T cells from cord blood	blood
14	chr3:59978800-59983400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr3:59980000-59980800	Enhancers	H9 Cell Line	embryonic stem cell
16	chr3:59980000-59980800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:59980200-59980800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr3:59980200-59980800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:59980200-59981000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr3:59980400-59980800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr3:59980400-59980800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:59980400-59980800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:59980600-59981800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:59980600-59982800	Enhancers	Fetal Lung	lung
25	chr3:59980600-59983200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:59980600-59992800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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