Variant report

Variant	rs17306795
Chromosome Location	chr19:38253790-38253791
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10406856	0.90[EUR][1000 genomes]
rs10418133	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10421572	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10422056	0.91[CHB][hapmap]
rs10425671	0.91[CHB][hapmap]
rs10426553	0.89[EUR][1000 genomes]
rs10426712	0.89[EUR][1000 genomes]
rs11083439	0.91[CHB][hapmap]
rs11668434	0.90[CHB][hapmap]
rs11668558	0.90[CHB][hapmap]
rs11672077	1.00[CHB][hapmap]
rs11883392	0.91[CHB][hapmap]
rs17306508	0.90[CHB][hapmap]
rs1871197	1.00[CHB][hapmap]
rs2045909	0.90[CHB][hapmap]
rs2160640	0.90[CHB][hapmap]
rs2382622	0.87[EUR][1000 genomes]
rs241937	0.90[CHB][hapmap]
rs241940	0.90[CHB][hapmap]
rs241941	0.91[CHB][hapmap]
rs241942	0.90[CHB][hapmap]
rs241948	0.90[CHB][hapmap]
rs241951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2927743	0.84[CEU][hapmap]
rs2972456	1.00[CHB][hapmap]
rs2972459	1.00[CHB][hapmap]
rs35462777	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752365	0.91[CHB][hapmap]
rs3894129	0.90[CHB][hapmap]
rs4482404	0.90[CHB][hapmap]
rs4802132	0.90[EUR][1000 genomes]
rs4802133	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs4802134	0.91[CHB][hapmap]
rs4802137	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55970469	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs56851463	0.90[EUR][1000 genomes]
rs57268445	0.90[EUR][1000 genomes]
rs6508738	1.00[CHB][hapmap]
rs6508747	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6508750	1.00[CEU][hapmap]
rs697433	0.90[CHB][hapmap]
rs7245957	0.87[EUR][1000 genomes]
rs7254170	1.00[CHB][hapmap]
rs7254828	0.90[CHB][hapmap]
rs8100684	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs8101131	0.90[EUR][1000 genomes]
rs8111400	0.91[CHB][hapmap]
rs856302	0.90[CHB][hapmap]
rs953370	1.00[CEU][hapmap]

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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17306795	AC012309.5	cis	Thyroid	GTEx
rs17306795	AC012309.5	cis	Artery Tibial	GTEx
rs17306795	AC012309.5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38230800-38259800	Weak transcription	Fetal Thymus	thymus
2	chr19:38231000-38258200	Weak transcription	Brain Anterior Caudate	brain
3	chr19:38231000-38258400	Weak transcription	Fetal Kidney	kidney
4	chr19:38231000-38258800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:38231000-38260400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:38231400-38255800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr19:38231400-38259400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr19:38231400-38259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:38231800-38257600	Weak transcription	HSMM	muscle
10	chr19:38231800-38258200	Weak transcription	HSMMtube	muscle
11	chr19:38231800-38269200	Weak transcription	Fetal Brain Male	brain
12	chr19:38232400-38254000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:38232400-38255600	Weak transcription	Psoas Muscle	Psoas
14	chr19:38232400-38256600	Weak transcription	Dnd41	blood
15	chr19:38236400-38269400	Weak transcription	Aorta	Aorta
16	chr19:38237000-38260400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:38238800-38254000	Weak transcription	Fetal Brain Female	brain
18	chr19:38238800-38269400	Weak transcription	Small Intestine	intestine
19	chr19:38239000-38269400	Weak transcription	Colonic Mucosa	Colon
20	chr19:38239400-38256600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:38239400-38257400	Weak transcription	Brain Angular Gyrus	brain
22	chr19:38242200-38258400	Weak transcription	NHDF-Ad	bronchial
23	chr19:38242800-38269000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:38243000-38258200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:38243600-38257200	Weak transcription	Fetal Lung	lung
26	chr19:38245200-38258200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr19:38246200-38258400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:38246800-38259600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:38246800-38259800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr19:38247400-38258200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr19:38247400-38259800	Weak transcription	Placenta	Placenta
32	chr19:38247800-38260000	Weak transcription	Osteobl	bone
33	chr19:38247800-38269200	Weak transcription	Hela-S3	cervix
34	chr19:38248400-38264600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr19:38248800-38269400	Weak transcription	NH-A	brain
36	chr19:38249000-38254200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr19:38249000-38259000	Weak transcription	Thymus	Thymus
38	chr19:38249200-38254800	ZNF genes & repeats	Liver	Liver
39	chr19:38249200-38269000	Weak transcription	Spleen	Spleen
40	chr19:38249400-38258200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr19:38249800-38269400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr19:38250400-38254600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr19:38250400-38255000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:38250400-38259600	Weak transcription	Esophagus	oesophagus
45	chr19:38250600-38254400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr19:38250600-38254800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr19:38250600-38262600	Strong transcription	Stomach Smooth Muscle	stomach
48	chr19:38250600-38264000	Strong transcription	Primary T cells from cord blood	blood
49	chr19:38250600-38264400	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:38250600-38265000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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