Variant report

Variant	rs4803551
Chromosome Location	chr19:38399461-38399462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr19:38398209-38399718	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:38396652-38400700	IMR90	lung:	n/a	n/a
3	EBF1	chr19:38399448-38399642	GM12878	blood:	n/a	n/a
4	MAX	chr19:38396216-38399888	A549	lung:	n/a	chr19:38398162-38398171 chr19:38399338-38399348 chr19:38397081-38397090 chr19:38397082-38397089

No.	Distal block	Cell Line	Cell type
1	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38399136..38401318-chr19:38404847..38407238,2	MCF-7	breast:
3	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:

Variant related genes	Relation type
WDR87	TF binding region
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10404159	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10404567	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs10415399	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10415548	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10420746	0.88[CEU][hapmap]
rs11083441	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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];0.82[EUR][1000 genomes]
rs12608883	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1291	0.88[CEU][hapmap]
rs12973580	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12974225	0.88[CEU][hapmap]
rs1643460	0.82[EUR][1000 genomes]
rs1643461	0.86[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];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2075281	0.88[CEU][hapmap]
rs241932	0.88[CEU][hapmap]
rs28460297	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2909093	0.82[CEU][hapmap]
rs2909098	0.88[CEU][hapmap]
rs2972437	0.88[CEU][hapmap]
rs2972438	0.88[CEU][hapmap]
rs2972439	0.88[CEU][hapmap]
rs3095726	0.82[CEU][hapmap]
rs353410	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353411	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.91[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802144	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802147	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802151	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803524	0.88[CEU][hapmap]
rs4803573	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[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];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs705494	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705495	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705499	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250409	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs8102579	0.88[CEU][hapmap]
rs8108434	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109053	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109835	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8110284	0.87[CEU][hapmap]
rs8112706	0.87[CEU][hapmap]
rs8113273	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8113521	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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:3 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4803551	PAFAH1B3	cis	cerebellum	SCAN
rs4803551	HIF3A	cis	parietal	SCAN
rs4803551	PHLDB3	cis	cerebellum	SCAN
rs4803551	AC012309.5	cis	Artery Tibial	GTEx
rs4803551	CBLC	cis	parietal	SCAN
rs4803551	DMPK	cis	parietal	SCAN
rs4803551	PHLDB3	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38396400-38400600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:38397000-38401000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr19:38398200-38399600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:38398200-38399800	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr19:38398400-38399600	Flanking Active TSS	Primary B cells from peripheral blood	blood
6	chr19:38398400-38399600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:38398400-38399600	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr19:38398400-38399800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr19:38398400-38399800	Flanking Active TSS	Dnd41	blood
10	chr19:38398400-38399800	Flanking Active TSS	Osteobl	bone
11	chr19:38398600-38399600	Flanking Active TSS	A549	lung
12	chr19:38398600-38399800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:38398600-38399800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr19:38398600-38399800	Enhancers	Left Ventricle	heart
15	chr19:38398600-38399800	Enhancers	Spleen	Spleen
16	chr19:38398600-38422600	Weak transcription	Aorta	Aorta
17	chr19:38398800-38399800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr19:38398800-38399800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:38398800-38399800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr19:38398800-38399800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr19:38398800-38399800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr19:38398800-38399800	Enhancers	Liver	Liver
23	chr19:38398800-38399800	Enhancers	Brain Substantia Nigra	brain
24	chr19:38398800-38399800	Enhancers	Gastric	stomach
25	chr19:38398800-38399800	Enhancers	Right Ventricle	heart
26	chr19:38398800-38399800	Enhancers	Small Intestine	intestine
27	chr19:38398800-38399800	Flanking Active TSS	NHDF-Ad	bronchial
28	chr19:38398800-38400000	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr19:38398800-38400400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr19:38398800-38400400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr19:38398800-38400400	Enhancers	Fetal Muscle Trunk	muscle
32	chr19:38398800-38400400	Enhancers	Fetal Thymus	thymus
33	chr19:38398800-38400400	Enhancers	Pancreas	Pancrea
34	chr19:38398800-38400600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr19:38398800-38405200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:38399000-38399600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:38399000-38399600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:38399000-38399600	Enhancers	Colonic Mucosa	Colon
40	chr19:38399000-38399600	Enhancers	Right Atrium	heart
41	chr19:38399000-38399800	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr19:38399000-38399800	Enhancers	Brain Angular Gyrus	brain
43	chr19:38399000-38400000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:38399000-38400000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:38399000-38400200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr19:38399000-38400200	Enhancers	Fetal Brain Male	brain
47	chr19:38399000-38400400	Enhancers	H9 Cell Line	embryonic stem cell
48	chr19:38399000-38400400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:38399000-38400600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:38399000-38400800	Enhancers	HepG2	liver

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