Variant report

Variant	rs17206379
Chromosome Location	chr19:36902219-36902220
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10407850	0.87[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs10416742	0.95[GIH][hapmap];0.84[TSI][hapmap]
rs12459704	0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs12461529	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12462725	1.00[ASW][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2271842	1.00[ASW][hapmap];0.89[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385802	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857	1.00[ASW][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2945955	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]
rs2945956	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2945989	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]
rs2967508	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967511	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967516	0.81[ASN][1000 genomes]
rs2967519	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3098393	0.83[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs3111556	0.87[ASN][1000 genomes]
rs3810326	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4806294	0.84[CHB][hapmap]
rs56378871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61706074	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62112567	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62112568	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62112569	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62112624	0.87[ASN][1000 genomes]
rs62112631	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62112632	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62113869	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7251745	0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap]
rs7253122	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73043845	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73043902	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104241	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17206379	ZFP82	cis	lymphoblastoid	seeQTL
rs17206379	ZNF545	cis	multi-tissue	Pritchard
rs17206379	ZFP14	cis	lymphoblastoid	seeQTL
rs17206379	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs17206379	LINC00665	cis	Muscle Skeletal	GTEx
rs17206379	LINC00665	cis	Nerve Tibial	GTEx
rs17206379	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:91 , 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	chr19:36894400-36902600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:36895000-36908200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr19:36896600-36908200	Weak transcription	Right Ventricle	heart
14	chr19:36896600-36908400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:36897200-36908200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:36898400-36902400	ZNF genes & repeats	Ovary	ovary
17	chr19:36898400-36904400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
18	chr19:36898400-36904600	ZNF genes & repeats	Primary B cells from cord blood	blood
19	chr19:36898400-36904600	ZNF genes & repeats	Liver	Liver
20	chr19:36898400-36906800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:36898400-36908600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr19:36899000-36902800	ZNF genes & repeats	Fetal Intestine Small	intestine
23	chr19:36899000-36904400	ZNF genes & repeats	Brain Germinal Matrix	brain
24	chr19:36899000-36908200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr19:36899200-36903600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:36899200-36908400	Weak transcription	NH-A	brain
27	chr19:36899600-36904000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:36899800-36905600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:36899800-36908200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr19:36900000-36908200	Weak transcription	HUVEC	blood vessel
31	chr19:36900200-36902400	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr19:36900200-36902600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:36900200-36903600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr19:36900400-36903200	Weak transcription	HSMM	muscle
35	chr19:36900400-36903400	Weak transcription	Osteobl	bone
36	chr19:36900400-36908200	Weak transcription	Brain Substantia Nigra	brain
37	chr19:36900400-36908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:36900600-36908000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr19:36900800-36903200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:36900800-36903200	Weak transcription	Adipose Nuclei	Adipose
41	chr19:36900800-36903400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr19:36900800-36903400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr19:36900800-36903600	Weak transcription	Brain Anterior Caudate	brain
44	chr19:36900800-36908200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr19:36900800-36908400	Weak transcription	Small Intestine	intestine
46	chr19:36901000-36903400	Weak transcription	Aorta	Aorta
47	chr19:36901000-36903400	Weak transcription	Brain Angular Gyrus	brain
48	chr19:36901000-36903600	Weak transcription	Psoas Muscle	Psoas
49	chr19:36901000-36903600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr19:36901000-36903600	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links