Variant report

Variant	rs2319156
Chromosome Location	chr19:39686675-39686676
allele	A/G
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	GABPA	chr19:39686447-39686999	MCF-7	breast:	n/a	n/a
2	MYC	chr19:39686599-39686683	MCF-7	breast:	n/a	n/a
3	ELF1	chr19:39686412-39686822	MCF-7	breast:	n/a	n/a
4	ZEB1	chr19:39686452-39686738	GM12878	blood:	n/a	chr19:39686550-39686559
5	NR2F2	chr19:39686421-39686841	MCF-7	breast:	n/a	chr19:39686693-39686708
6	GABPA	chr19:39686462-39686917	MCF-7	breast:	n/a	n/a
7	ZBTB7A	chr19:39686657-39686797	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39677174..39681975-chr19:39683439..39687085,6	MCF-7	breast:
2	chr19:39678151..39679810-chr19:39685956..39687541,2	MCF-7	breast:
3	chr19:39645920..39648679-chr19:39684558..39687537,2	MCF-7	breast:
4	chr19:39684528..39687372-chr19:39688107..39690948,3	MCF-7	breast:

Variant related genes	Relation type
NCCRP1	TF binding region
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11083511	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083512	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083513	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083514	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11668945	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672471	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672475	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672479	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672787	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12462614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609028	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12609203	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12610064	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12610093	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12610618	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12974074	0.87[CHB][hapmap]
rs12974792	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12976040	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1808652	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2013626	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2319154	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2319155	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2873914	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58016205	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58278424	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7508321	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8100659	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8103222	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8103224	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106521	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs892015	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs892016	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv1796470	chr19:39679379-39714631	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2319156	CCDC8	cis	parietal	SCAN
rs2319156	ZNF229	cis	parietal	SCAN
rs2319156	ZNF229	cis	cerebellum	SCAN
rs2319156	B9D2	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39657800-39687600	Weak transcription	Right Atrium	heart
2	chr19:39678600-39687400	Weak transcription	Spleen	Spleen
3	chr19:39685000-39690000	Enhancers	A549	lung
4	chr19:39685400-39687600	Enhancers	Pancreas	Pancrea
5	chr19:39685400-39688800	Bivalent Enhancer	Placenta	Placenta
6	chr19:39685600-39686800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr19:39685600-39686800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
8	chr19:39685600-39688000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:39685600-39688200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
10	chr19:39685600-39688200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr19:39685600-39688200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
12	chr19:39685800-39686800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:39685800-39687000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:39685800-39687000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
15	chr19:39685800-39687200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:39685800-39687400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
17	chr19:39685800-39687400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:39685800-39688200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr19:39686000-39686800	Bivalent Enhancer	Stomach Mucosa	stomach
20	chr19:39686000-39687000	Enhancers	Primary T cells from cord blood	blood
21	chr19:39686000-39687400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:39686000-39687600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:39686000-39687600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:39686000-39688200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:39686000-39688400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:39686200-39688000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:39686200-39688000	Weak transcription	Hela-S3	cervix
28	chr19:39686400-39687400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:39686400-39687400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
30	chr19:39686400-39688400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
31	chr19:39686600-39686800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:39686600-39686800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:39686600-39686800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
34	chr19:39686600-39686800	Flanking Active TSS	Esophagus	oesophagus
35	chr19:39686600-39686800	Enhancers	Gastric	stomach
36	chr19:39686600-39686800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr19:39686600-39686800	Enhancers	HMEC	breast
38	chr19:39686600-39687000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
39	chr19:39686600-39687000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
40	chr19:39686600-39687000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
41	chr19:39686600-39687000	Bivalent Enhancer	Fetal Thymus	thymus
42	chr19:39686600-39687400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:39686600-39687400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:39686600-39687400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:39686600-39687400	Bivalent Enhancer	Fetal Intestine Large	intestine
46	chr19:39686600-39688000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr19:39686600-39688000	Bivalent Enhancer	NHEK	skin
48	chr19:39686600-39688200	Bivalent Enhancer	Fetal Intestine Small	intestine

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