Variant report

Variant	rs4808172
Chromosome Location	chr19:19100787-19100788
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19100779-19101245	H1-neurons	neurons:	n/a	n/a
2	FOSL2	chr19:19100579-19101264	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:19100000-19101400	U87	brain:	n/a	n/a
4	BCL3	chr19:19100705-19101625	K562	blood:	n/a	chr19:19101367-19101375
5	POLR2A	chr19:19100231-19101401	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr19:19100448-19101703	HL-60	blood:	n/a	n/a
7	POLR2A	chr19:19100132-19101475	MCF-7	breast:	n/a	n/a
8	POLR2A	chr19:19100510-19101751	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr19:19100459-19101657	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:19100639-19101685	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:19100090-19101643	A549	lung:	n/a	n/a
12	POLR2A	chr19:19100530-19101696	K562	blood:	n/a	n/a
13	POLR2A	chr19:19100496-19101706	K562	blood:	n/a	n/a
14	CTCF	chr19:19100720-19100870	HEK293	kidney:	n/a	chr19:19100790-19100798
15	POLR2A	chr19:19100011-19101562	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr19:19100749-19100956	HCT-116	colon:	n/a	n/a
17	POLR2A	chr19:19100598-19101637	K562	blood:	n/a	n/a
18	POLR2A	chr19:19099946-19100795	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr19:19100525-19101612	GM12891	blood:	n/a	n/a
20	NFATC1	chr19:19100635-19101062	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:19100068-19101488	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr19:19100540-19101737	GM12891	blood:	n/a	n/a
23	POLR2A	chr19:19100191-19101461	GM12878	blood:	n/a	n/a
24	CHD2	chr19:19100730-19100794	K562	blood:	n/a	n/a
25	POLR2A	chr19:19100684-19101203	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr19:19100623-19101523	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr19:19100000-19101464	U87	brain:	n/a	n/a
28	MTA3	chr19:19099927-19101533	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:19100647-19101174	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr19:19099930-19101770	SK-N-MC	brain:	n/a	n/a
31	POLR2A	chr19:19100088-19102888	K562	blood:	n/a	n/a
32	PML	chr19:19100257-19101453	GM12878	blood:	n/a	chr19:19101182-19101190
33	POLR2A	chr19:19100114-19101675	GM12891	blood:	n/a	n/a
34	ATF2	chr19:19100783-19101208	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:19100283-19102204	HL-60	blood:	n/a	n/a
36	POLR2A	chr19:19100780-19101701	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr19:19100059-19101646	PFSK-1	brain:	n/a	n/a
38	STAT5A	chr19:19100398-19101320	GM12878	blood:	n/a	chr19:19100767-19100775 chr19:19101068-19101080
39	POLR2A	chr19:19100049-19101659	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:19100576-19101642	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:19100658-19101199	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr19:19100236-19101610	HepG2	liver:	n/a	n/a
43	POLR2A	chr19:19100564-19101653	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:19100142-19101703	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr19:19100169-19101732	GM12892	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19099305..19102487-chr19:19102568..19107094,5	MCF-7	breast:
2	chr19:18896840..18897549-chr19:19100206..19100956,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269131	TF binding region
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10403272	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10416783	0.85[CEU][hapmap]
rs1079543	0.85[CEU][hapmap];0.86[MEX][hapmap]
rs10854005	0.89[ASW][hapmap];0.90[CEU][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11085249	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11666340	0.83[ASW][hapmap];0.90[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs11670204	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs11671696	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878368	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12016	0.85[CEU][hapmap]
rs12979565	0.90[CEU][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs1859267	0.89[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2013813	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2240094	0.85[CEU][hapmap]
rs2240095	0.81[AMR][1000 genomes]
rs2269869	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2872394	0.83[ASW][hapmap];0.90[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap]
rs3180770	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs3787041	0.85[JPT][hapmap]
rs4808176	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4808895	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4808900	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808905	0.83[AFR][1000 genomes]
rs4808906	0.85[CEU][hapmap]
rs4808907	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs4808913	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs4808916	0.85[JPT][hapmap]
rs4808917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6511010	0.90[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs7249453	0.81[AFR][1000 genomes]
rs7252615	0.91[ASN][1000 genomes]
rs7253244	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs8104799	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs8109654	0.87[AMR][1000 genomes]
rs8110629	0.90[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs8111634	0.85[CEU][hapmap];0.80[TSI][hapmap]
rs929215	0.90[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv2435	chr19:19077432-19122579	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4808172	TMEM161A	cis	Muscle Skeletal	GTEx
rs4808172	MED26	cis	cerebellum	SCAN
rs4808172	CPAMD8	cis	cerebellum	SCAN
rs4808172	SUGP1	cis	parietal	SCAN
rs4808172	KIAA1683	cis	cerebellum	SCAN
rs4808172	TSSK6	cis	cerebellum	SCAN
rs4808172	ANKLE1	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19084200-19107800	Weak transcription	Right Atrium	heart
2	chr19:19096200-19101600	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr19:19096200-19104000	Weak transcription	Primary B cells from cord blood	blood
4	chr19:19096400-19100800	Weak transcription	Fetal Brain Female	brain
5	chr19:19096400-19101000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:19096400-19102200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr19:19096400-19103400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:19096400-19103600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr19:19096600-19101400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:19096600-19103400	Weak transcription	NH-A	brain
11	chr19:19096800-19101200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:19096800-19102400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:19096800-19104000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr19:19097000-19101800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:19097600-19101000	Weak transcription	Spleen	Spleen
16	chr19:19097600-19101200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr19:19097600-19101800	Weak transcription	NHLF	lung
18	chr19:19097600-19102000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr19:19097600-19102400	Weak transcription	Left Ventricle	heart
20	chr19:19097600-19103400	Weak transcription	HUVEC	blood vessel
21	chr19:19097600-19103600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr19:19097800-19101000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr19:19097800-19101200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:19097800-19101200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:19098000-19100800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:19098000-19100800	Weak transcription	Fetal Lung	lung
27	chr19:19098000-19101000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:19098000-19101000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:19098000-19101000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr19:19098000-19101000	Weak transcription	Brain Anterior Caudate	brain
31	chr19:19098000-19101000	Weak transcription	Brain Hippocampus Middle	brain
32	chr19:19098000-19101000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:19098000-19101000	Weak transcription	Lung	lung
34	chr19:19098000-19101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr19:19098000-19101200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr19:19098000-19101200	Weak transcription	Brain Substantia Nigra	brain
37	chr19:19098000-19101400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr19:19098000-19101400	Weak transcription	Liver	Liver
39	chr19:19098000-19101400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr19:19098000-19101400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr19:19098000-19101400	Weak transcription	NHDF-Ad	bronchial
42	chr19:19098000-19101600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:19098000-19101800	Weak transcription	Fetal Brain Male	brain
44	chr19:19098000-19101800	Weak transcription	Pancreas	Pancrea
45	chr19:19098000-19101800	Weak transcription	HMEC	breast
46	chr19:19098000-19102000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr19:19098000-19102000	Weak transcription	Brain Angular Gyrus	brain
48	chr19:19098000-19102000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr19:19098000-19102000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr19:19098000-19102000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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