Variant report

Variant	rs2945955
Chromosome Location	chr19:36889149-36889150
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10403738	0.92[CHB][hapmap]
rs10407850	0.90[CHB][hapmap]
rs10416509	0.92[CHB][hapmap]
rs10416742	0.90[CHB][hapmap]
rs10416925	0.90[CHB][hapmap]
rs12459704	0.90[CHB][hapmap]
rs12461077	0.83[CHB][hapmap]
rs12461529	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12462725	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17206379	0.88[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385802	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2857	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945989	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967508	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967511	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967514	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2967516	0.83[ASN][1000 genomes]
rs2967519	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098393	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3111555	0.82[ASN][1000 genomes]
rs3111556	0.89[ASN][1000 genomes]
rs3810326	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4806284	0.92[CHB][hapmap]
rs56378871	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61706074	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62112567	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62112568	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62112569	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62112624	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62112631	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62112632	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62113869	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7251745	0.90[CHB][hapmap]
rs7253122	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73043845	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73043902	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104241	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8111860	0.90[CHB][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	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1066026	chr19:36878441-36947928	ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2945955	CTD-3162L10.1	cis	Nerve Tibial	GTEx
rs2945955	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs2945955	ZNF545	cis	multi-tissue	Pritchard
rs2945955	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx
rs2945955	LINC00665	cis	Nerve Tibial	GTEx
rs2945955	LINC00665	cis	Muscle Skeletal	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36880400-36892800	ZNF genes & repeats	Liver	Liver
2	chr19:36880400-36893200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:36880400-36904600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:36880600-36893000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
5	chr19:36880600-36893200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:36881400-36892800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:36882000-36891800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
8	chr19:36882200-36890400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
9	chr19:36882200-36892800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr19:36882200-36908800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:36882400-36890600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:36882400-36892000	ZNF genes & repeats	Fetal Brain Female	brain
13	chr19:36882400-36892800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:36882400-36896600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:36882400-36907600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:36882600-36889600	ZNF genes & repeats	Fetal Intestine Large	intestine
17	chr19:36882600-36890400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:36882600-36893600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr19:36882600-36904200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:36882800-36893000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:36883000-36890600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:36883000-36892800	ZNF genes & repeats	Ovary	ovary
23	chr19:36883000-36893000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:36883000-36893400	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr19:36883000-36905200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
26	chr19:36883200-36892800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:36883600-36893800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
28	chr19:36884800-36890000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:36885600-36908000	Weak transcription	K562	blood
30	chr19:36886000-36890600	ZNF genes & repeats	Fetal Stomach	stomach
31	chr19:36886200-36893800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:36886400-36889600	Weak transcription	NHDF-Ad	bronchial
33	chr19:36886400-36890600	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr19:36886400-36901000	Weak transcription	Stomach Mucosa	stomach
35	chr19:36886600-36889400	Weak transcription	Fetal Brain Male	brain
36	chr19:36886600-36889400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr19:36886600-36889600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:36886600-36889600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr19:36886600-36889600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr19:36886600-36889600	Weak transcription	HSMMtube	muscle
41	chr19:36886600-36890000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr19:36886600-36890200	Weak transcription	Brain Angular Gyrus	brain
43	chr19:36886600-36890200	Weak transcription	Brain Substantia Nigra	brain
44	chr19:36886600-36890200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr19:36886600-36890200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:36886600-36890200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:36886600-36890200	Weak transcription	NH-A	brain
48	chr19:36886600-36891200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr19:36886600-36891400	Weak transcription	Brain Anterior Caudate	brain
50	chr19:36886600-36891400	Weak transcription	Fetal Kidney	kidney

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