Variant report

Variant	rs8108434
Chromosome Location	chr19:38411090-38411091
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38402813..38405228-chr19:38408699..38411381,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10404159	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10404567	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs10415399	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10415548	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10420746	0.88[CEU][hapmap]
rs11083441	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1119229	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs12608883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1291	0.88[CEU][hapmap]
rs12973580	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12974225	0.88[CEU][hapmap]
rs1643460	0.84[EUR][1000 genomes]
rs1643461	0.88[EUR][1000 genomes]
rs1643466	0.87[CEU][hapmap]
rs1643467	0.87[CEU][hapmap]
rs1643468	0.87[CEU][hapmap]
rs1725481	0.88[CEU][hapmap]
rs1725482	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs1725499	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075281	0.88[CEU][hapmap]
rs241932	0.88[CEU][hapmap]
rs28460297	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972439	0.88[CEU][hapmap]
rs3095726	0.82[CEU][hapmap]
rs353410	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs353411	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs353414	0.87[CEU][hapmap]
rs353415	0.88[CEU][hapmap]
rs353423	0.87[CEU][hapmap]
rs3786869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3865514	1.00[YRI][hapmap]
rs4239516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802144	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802151	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4803524	0.88[CEU][hapmap]
rs4803551	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803573	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705491	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs705492	0.88[CEU][hapmap]
rs705493	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs705494	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705495	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705499	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7250409	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs8102579	0.88[CEU][hapmap]
rs8109053	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109835	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110284	0.87[CEU][hapmap]
rs8112706	0.87[CEU][hapmap]
rs8113273	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8113521	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs833895	0.87[CEU][hapmap]
rs833926	0.88[CEU][hapmap]
rs856300	0.82[CEU][hapmap]
rs856304	0.88[CEU][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	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
2	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
3	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs8108434	AC012309.5	cis	Artery Tibial	GTEx
rs8108434	CBLC	cis	parietal	SCAN
rs8108434	PAFAH1B3	cis	cerebellum	SCAN
rs8108434	DMPK	cis	parietal	SCAN
rs8108434	HIF3A	cis	parietal	SCAN
rs8108434	PHLDB3	cis	cerebellum	SCAN
rs8108434	PHLDB3	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398600-38422600	Weak transcription	Aorta	Aorta
2	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:38399000-38418400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:38399000-38422400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:38399200-38411400	Weak transcription	NHEK	skin
6	chr19:38399200-38411800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:38399200-38411800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr19:38399200-38415600	Weak transcription	Hela-S3	cervix
9	chr19:38399200-38416000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:38399200-38422400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:38399200-38422600	Weak transcription	Fetal Lung	lung
12	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:38399600-38411400	Weak transcription	Esophagus	oesophagus
14	chr19:38399600-38422000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:38399600-38424000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:38399600-38424200	Weak transcription	Right Atrium	heart
17	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:38399800-38411600	Weak transcription	Lung	lung
19	chr19:38399800-38413800	Weak transcription	Liver	Liver
20	chr19:38399800-38417200	Weak transcription	Ovary	ovary
21	chr19:38399800-38421200	Weak transcription	Gastric	stomach
22	chr19:38399800-38421800	Weak transcription	Left Ventricle	heart
23	chr19:38399800-38422400	Weak transcription	Fetal Brain Female	brain
24	chr19:38399800-38422600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr19:38400000-38411200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr19:38400000-38411400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr19:38400000-38422000	Weak transcription	HSMM	muscle
28	chr19:38400400-38411200	Weak transcription	Brain Germinal Matrix	brain
29	chr19:38400400-38416800	Weak transcription	Pancreas	Pancrea
30	chr19:38400400-38419400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:38400400-38421800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr19:38400600-38411400	Weak transcription	Osteobl	bone
33	chr19:38400600-38422000	Weak transcription	HSMMtube	muscle
34	chr19:38400600-38422400	Weak transcription	HUVEC	blood vessel
35	chr19:38400800-38411400	Weak transcription	NH-A	brain
36	chr19:38400800-38422400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr19:38401000-38416600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:38401000-38421600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr19:38401200-38416800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr19:38401200-38421200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr19:38401800-38411200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:38401800-38411200	Weak transcription	HMEC	breast
43	chr19:38402000-38416800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr19:38402000-38422600	Weak transcription	Fetal Brain Male	brain
45	chr19:38404200-38411800	Weak transcription	Fetal Stomach	stomach
46	chr19:38404200-38416800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr19:38405200-38422600	Weak transcription	Right Ventricle	heart
48	chr19:38405600-38422800	Weak transcription	Colon Smooth Muscle	Colon
49	chr19:38406000-38411200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr19:38406000-38411400	Weak transcription	Primary monocytes fromperipheralblood	blood

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