Variant report

Variant	rs2945989
Chromosome Location	chr19:36903262-36903263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10407850	0.93[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs10416742	0.95[GIH][hapmap];0.81[TSI][hapmap]
rs12459704	0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap]
rs12461529	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12462725	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17206379	0.89[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271842	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385802	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2945955	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]
rs2945956	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967508	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967511	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967514	1.00[YRI][hapmap]
rs2967516	0.82[ASN][1000 genomes]
rs2967519	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3098393	0.83[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs3111555	0.81[ASN][1000 genomes]
rs3111556	0.88[ASN][1000 genomes]
rs3810326	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56378871	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61706074	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62112567	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112568	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112569	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112624	0.88[ASN][1000 genomes]
rs62112631	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62112632	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62113869	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251745	0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs7253122	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73043845	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73043902	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104241	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1067101	chr19:36901010-36956251	ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2945989	KIAA1559	cis	multi-tissue	Pritchard
rs2945989	ZNF222	cis	parietal	SCAN
rs2945989	ZFP82	cis	lymphoblastoid	seeQTL
rs2945989	ZNF527	cis	cerebellum	SCAN
rs2945989	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx
rs2945989	ZFP14	cis	lymphoblastoid	seeQTL
rs2945989	LINC00665	cis	Muscle Skeletal	GTEx
rs2945989	LINC00665	cis	Nerve Tibial	GTEx
rs2945989	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs2945989	ZNF545	cis	multi-tissue	Pritchard
rs2945989	ZNF781	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36880400-36904600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:36882200-36908800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:36882400-36907600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:36882600-36904200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:36883000-36905200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
6	chr19:36885600-36908000	Weak transcription	K562	blood
7	chr19:36889800-36908200	Weak transcription	HepG2	liver
8	chr19:36891000-36904800	Strong transcription	Dnd41	blood
9	chr19:36891800-36908200	Weak transcription	Fetal Heart	heart
10	chr19:36891800-36908200	Weak transcription	Hela-S3	cervix
11	chr19:36895000-36908200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr19:36896600-36908200	Weak transcription	Right Ventricle	heart
13	chr19:36896600-36908400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:36897200-36908200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:36898400-36904400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
16	chr19:36898400-36904600	ZNF genes & repeats	Primary B cells from cord blood	blood
17	chr19:36898400-36904600	ZNF genes & repeats	Liver	Liver
18	chr19:36898400-36906800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:36898400-36908600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr19:36899000-36904400	ZNF genes & repeats	Brain Germinal Matrix	brain
21	chr19:36899000-36908200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr19:36899200-36903600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:36899200-36908400	Weak transcription	NH-A	brain
24	chr19:36899600-36904000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr19:36899800-36905600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:36899800-36908200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:36900000-36908200	Weak transcription	HUVEC	blood vessel
28	chr19:36900200-36903600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:36900400-36903400	Weak transcription	Osteobl	bone
30	chr19:36900400-36908200	Weak transcription	Brain Substantia Nigra	brain
31	chr19:36900400-36908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:36900600-36908000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr19:36900800-36903400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr19:36900800-36903400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr19:36900800-36903600	Weak transcription	Brain Anterior Caudate	brain
36	chr19:36900800-36908200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr19:36900800-36908400	Weak transcription	Small Intestine	intestine
38	chr19:36901000-36903400	Weak transcription	Aorta	Aorta
39	chr19:36901000-36903400	Weak transcription	Brain Angular Gyrus	brain
40	chr19:36901000-36903600	Weak transcription	Psoas Muscle	Psoas
41	chr19:36901000-36903600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr19:36901000-36903600	Weak transcription	NHLF	lung
43	chr19:36901000-36903800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr19:36901000-36907400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr19:36901000-36908000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:36901000-36908000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr19:36901000-36908400	Weak transcription	Fetal Kidney	kidney
48	chr19:36901000-36908400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr19:36901000-36908400	Weak transcription	HSMMtube	muscle
50	chr19:36901200-36903400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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