Variant report

Variant	rs2659095
Chromosome Location	chr19:51505857-51505858
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	USF1	chr19:51505827-51506329	ECC-1	luminal epithelium:	n/a	n/a
2	JUN	chr19:51505735-51506306	K562	blood:	n/a	n/a
3	CREB1	chr19:51505675-51506406	H1-hESC	embryonic stem cell:	n/a	n/a
4	ELK1	chr19:51505823-51506011	K562	blood:	n/a	n/a
5	CTCF	chr19:51505720-51505870	NHEK	skin:	n/a	n/a
6	USF2	chr19:51505852-51506231	K562	blood:	n/a	n/a
7	NR2F2	chr19:51505743-51506390	K562	blood:	n/a	n/a
8	JUND	chr19:51505711-51506311	H1-hESC	embryonic stem cell:	n/a	n/a
9	CREB1	chr19:51505827-51506320	A549	lung:	n/a	n/a
10	USF1	chr19:51505677-51506401	K562	blood:	n/a	n/a
11	RCOR1	chr19:51505709-51505906	K562	blood:	n/a	n/a
12	EGR1	chr19:51505526-51506049	K562	blood:	n/a	chr19:51505717-51505724 chr19:51505717-51505730 chr19:51505716-51505731
13	BACH1	chr19:51505857-51506062	H1-hESC	embryonic stem cell:	n/a	n/a
14	EGR1	chr19:51505334-51506467	HCT-116	colon:	n/a	chr19:51505717-51505724 chr19:51505717-51505730 chr19:51505716-51505731
15	ELF1	chr19:51505778-51506237	K562	blood:	n/a	n/a
16	USF1	chr19:51505828-51506294	H1-hESC	embryonic stem cell:	n/a	n/a
17	TEAD4	chr19:51505605-51506309	K562	blood:	n/a	n/a
18	ELF1	chr19:51505841-51506235	K562	blood:	n/a	n/a
19	IRF1	chr19:51505790-51506367	K562	blood:	n/a	n/a
20	MYC	chr19:51505722-51506268	K562	blood:	n/a	n/a
21	TBL1XR1	chr19:51505774-51506239	K562	blood:	n/a	n/a
22	MAZ	chr19:51505320-51506299	K562	blood:	n/a	chr19:51505421-51505431
23	POLR2A	chr19:51505616-51506050	K562	blood:	n/a	n/a
24	CEBPB	chr19:51505625-51506268	K562	blood:	n/a	n/a
25	GTF2F1	chr19:51505761-51505942	K562	blood:	n/a	n/a
26	MAX	chr19:51505631-51506180	A549	lung:	n/a	n/a
27	POLR2A	chr19:51504104-51506325	HCT-116	colon:	n/a	n/a
28	CREB1	chr19:51505718-51506458	K562	blood:	n/a	n/a
29	CREB1	chr19:51505739-51506327	H1-hESC	embryonic stem cell:	n/a	n/a
30	JUND	chr19:51505676-51506360	K562	blood:	n/a	n/a
31	E2F6	chr19:51505736-51506038	K562	blood:	n/a	n/a
32	SP1	chr19:51505750-51506343	A549	lung:	n/a	n/a
33	EP300	chr19:51505758-51506258	K562	blood:	n/a	n/a
34	USF1	chr19:51505769-51506253	K562	blood:	n/a	n/a
35	USF2	chr19:51505811-51506260	H1-hESC	embryonic stem cell:	n/a	n/a
36	JUN	chr19:51505471-51506743	K562	blood:	n/a	n/a
37	CTCF	chr19:51505740-51505890	HMEC	breast:	n/a	n/a
38	ZBTB7A	chr19:51505028-51506314	K562	blood:	n/a	n/a
39	YY1	chr19:51505793-51506227	HCT-116	colon:	n/a	n/a
40	SPI1	chr19:51505857-51506145	K562	blood:	n/a	n/a
41	BHLHE40	chr19:51505735-51506365	K562	blood:	n/a	n/a
42	MAX	chr19:51505499-51506405	K562	blood:	n/a	n/a
43	ZBTB33	chr19:51505730-51506006	HCT-116	colon:	n/a	n/a
44	TBP	chr19:51505718-51506269	K562	blood:	n/a	n/a
45	MAX	chr19:51505768-51506312	K562	blood:	n/a	n/a
46	HMGN3	chr19:51505664-51506453	K562	blood:	n/a	n/a
47	JUN	chr19:51505724-51506300	K562	blood:	n/a	n/a
48	HCFC1	chr19:51505588-51506191	K562	blood:	n/a	n/a
49	EGR1	chr19:51505542-51506378	K562	blood:	n/a	chr19:51505717-51505724 chr19:51505717-51505730 chr19:51505716-51505731
50	CCNT2	chr19:51505837-51506215	K562	blood:	n/a	n/a

Variant related genes	Relation type
KLK8	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1061368	0.80[AMR][1000 genomes]
rs1532901	0.85[CEU][hapmap]
rs1654559	0.84[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap]
rs1698	0.92[CEU][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs1701916	0.82[CEU][hapmap]
rs1701921	0.83[CEU][hapmap]
rs1722550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1829971	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2075696	0.81[AMR][1000 genomes]
rs2075802	0.85[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2222554	0.92[CEU][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap]
rs2569439	0.80[EUR][1000 genomes]
rs2569440	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2569443	0.88[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2569456	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659071	0.84[CEU][hapmap]
rs2659096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs268899	0.80[CEU][hapmap];0.80[GIH][hapmap];0.83[MEX][hapmap]
rs2691208	0.81[CHD][hapmap]
rs2691257	0.95[CEU][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs2739429	0.83[ASW][hapmap];0.88[CEU][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes]
rs6509509	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[ASN][1000 genomes]
rs906190	0.84[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][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	nsv1058277	chr19:51488544-51509847	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv912291	chr19:51505725-51537682	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2659095	RPS5	cis	parietal	SCAN
rs2659095	ZNF132	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51503200-51506000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr19:51503200-51506000	Flanking Active TSS	HMEC	breast
3	chr19:51503400-51506000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr19:51503400-51506000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr19:51503400-51506000	Flanking Active TSS	NHEK	skin
6	chr19:51503600-51506400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:51503800-51506200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:51504000-51506000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr19:51504200-51506000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:51504200-51506000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr19:51504200-51506400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr19:51504800-51506400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr19:51505000-51506000	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr19:51505200-51506000	Bivalent Enhancer	Fetal Muscle Leg	muscle
15	chr19:51505200-51506200	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr19:51505400-51506000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:51505400-51506400	Flanking Active TSS	K562	blood
18	chr19:51505600-51506000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:51505600-51506000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:51505600-51506000	Flanking Bivalent TSS/Enh	A549	lung
21	chr19:51505800-51506000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:51505800-51506000	Enhancers	Esophagus	oesophagus
23	chr19:51505800-51506200	Bivalent Enhancer	Placenta	Placenta
24	chr19:51505800-51506200	Bivalent Enhancer	Fetal Stomach	stomach
25	chr19:51505800-51506400	Enhancers	H1 Cell Line	embryonic stem cell

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