Variant report

Variant	rs7256692
Chromosome Location	chr19:39884917-39884918
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	POLR2A	chr19:39850716-39886400	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39884419-39885032	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39881608..39883265-chr19:39883392..39885863,2	MCF-7	breast:
2	chr19:39879787..39883867-chr19:39884525..39889123,13	K562	blood:

Variant related genes	Relation type
PAF1	TF binding region
ENSG00000063322	Chromatin interaction
ENSG00000006712	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10402122	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10403504	0.94[ASW][hapmap];0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10412877	0.87[ASW][hapmap];0.92[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10414216	0.94[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10423565	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10425594	0.87[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11665856	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672863	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12973448	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12977767	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs251864	0.90[AMR][1000 genomes]
rs3843755	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803235	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs565545	0.89[AMR][1000 genomes]
rs7250966	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253005	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
4	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
6	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
7	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7256692	TRAPPC6A	cis	parietal	SCAN
rs7256692	FOSB	cis	parietal	SCAN
rs7256692	BCAM	cis	cerebellum	SCAN
rs7256692	ZNF780A	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39883000-39888000	Weak transcription	Psoas Muscle	Psoas
2	chr19:39883000-39888200	Weak transcription	Right Atrium	heart
3	chr19:39883000-39888600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:39883000-39888600	Weak transcription	Small Intestine	intestine
5	chr19:39883000-39891800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:39883200-39887800	Weak transcription	HSMM	muscle
7	chr19:39883200-39888000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:39883200-39888000	Strong transcription	Fetal Intestine Small	intestine
9	chr19:39883200-39888200	Weak transcription	Fetal Heart	heart
10	chr19:39883200-39888200	Weak transcription	HUVEC	blood vessel
11	chr19:39883200-39888200	Weak transcription	NHEK	skin
12	chr19:39883200-39888600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:39883200-39891600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr19:39883200-39892400	Weak transcription	Fetal Brain Male	brain
15	chr19:39883200-39892400	Weak transcription	Fetal Kidney	kidney
16	chr19:39883400-39886200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr19:39883400-39886200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:39883400-39887000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:39883400-39887200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:39883400-39887800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:39883400-39888000	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr19:39883400-39888000	Strong transcription	Fetal Stomach	stomach
23	chr19:39883400-39888200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:39883600-39885800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr19:39883600-39885800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:39883600-39886400	Strong transcription	Fetal Thymus	thymus
27	chr19:39883600-39886800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:39883600-39886800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:39883600-39886800	Strong transcription	Fetal Muscle Leg	muscle
30	chr19:39883600-39887000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:39883800-39886800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr19:39883800-39888000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr19:39884000-39885800	Strong transcription	Spleen	Spleen
34	chr19:39884000-39886200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:39884000-39886800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:39884000-39886800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr19:39884000-39886800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:39884000-39886800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr19:39884000-39886800	Strong transcription	Fetal Brain Female	brain
40	chr19:39884000-39887000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr19:39884000-39887000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:39884000-39887000	Strong transcription	Adipose Nuclei	Adipose
43	chr19:39884000-39887400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr19:39884000-39888000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:39884000-39888000	Strong transcription	Fetal Intestine Large	intestine
46	chr19:39884000-39888000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr19:39884000-39888000	Strong transcription	Placenta	Placenta
48	chr19:39884000-39888000	Strong transcription	Thymus	Thymus
49	chr19:39884000-39888200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:39884200-39885000	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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