Variant report

Variant	rs7259067
Chromosome Location	chr19:41124931-41124932
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	POLR2A	chr19:41124821-41126123	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41124837..41127623-chr19:41128231..41131194,3	K562	blood:
2	chr19:41116781..41119658-chr19:41124114..41126032,2	MCF-7	breast:

Variant related genes	Relation type
LTBP4	TF binding region
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10402698	0.80[ASN][1000 genomes]
rs10403467	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10403833	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403963	0.86[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10405930	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10410606	0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1051303	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083561	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1131620	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11667706	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11667772	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11668582	0.89[EUR][1000 genomes]
rs12610819	0.86[CHD][hapmap];0.80[GIH][hapmap]
rs12611045	0.98[ASN][1000 genomes]
rs12980111	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1318544	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864074	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864078	0.87[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869712	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278246	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303727	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303729	0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2369006	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2604902	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28571670	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28649715	0.99[ASN][1000 genomes]
rs28655571	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392726	0.89[CHB][hapmap];0.93[CHD][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs393569	0.89[CHB][hapmap];0.85[CHD][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs396118	0.85[ASN][1000 genomes]
rs404584	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs406133	0.82[ASN][1000 genomes]
rs410101	0.85[CHD][hapmap]
rs413901	0.85[CHD][hapmap]
rs415075	0.84[ASN][1000 genomes]
rs420720	0.85[ASN][1000 genomes]
rs4803348	0.98[ASN][1000 genomes]
rs56353506	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7171	0.86[ASN][1000 genomes]
rs7254268	0.83[LWK][hapmap]
rs7257696	0.83[CHD][hapmap]
rs7259237	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259554	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107014	0.86[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs919307	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911721	chr19:41040334-41124931	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
13	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
15	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
16	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
17	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7259067	PGLYRP1	cis	cerebellum	SCAN
rs7259067	QPCTL	cis	cerebellum	SCAN
rs7259067	B9D2	cis	parietal	SCAN
rs7259067	ZNF296	cis	cerebellum	SCAN
rs7259067	CA11	cis	cerebellum	SCAN
rs7259067	CEACAM6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41106000-41136800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41116600-41137000	Weak transcription	Psoas Muscle	Psoas
3	chr19:41117000-41140200	Weak transcription	Brain Angular Gyrus	brain
4	chr19:41117400-41125200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:41120200-41127800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr19:41120400-41127000	Weak transcription	Brain Germinal Matrix	brain
7	chr19:41120400-41139800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:41120600-41125400	Weak transcription	Gastric	stomach
9	chr19:41120600-41129400	Weak transcription	Pancreas	Pancrea
10	chr19:41120600-41133000	Weak transcription	Fetal Brain Male	brain
11	chr19:41120800-41125200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:41120800-41127200	Weak transcription	Fetal Brain Female	brain
13	chr19:41120800-41128000	Weak transcription	Primary B cells from cord blood	blood
14	chr19:41120800-41128000	Weak transcription	Small Intestine	intestine
15	chr19:41120800-41139200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr19:41120800-41140200	Weak transcription	Brain Anterior Caudate	brain
17	chr19:41121000-41125000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:41121000-41125000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:41121000-41125000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:41121000-41125200	Weak transcription	Primary T cells from cord blood	blood
21	chr19:41121000-41125200	Weak transcription	Fetal Thymus	thymus
22	chr19:41121000-41125200	Weak transcription	Left Ventricle	heart
23	chr19:41121000-41125200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:41121000-41125200	Weak transcription	Stomach Mucosa	stomach
25	chr19:41121000-41125200	Weak transcription	A549	lung
26	chr19:41121000-41125400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr19:41121000-41125400	Weak transcription	Esophagus	oesophagus
28	chr19:41121000-41125600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:41121000-41125600	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:41121000-41129400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr19:41121200-41125200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr19:41121200-41125200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:41121200-41125200	Weak transcription	Thymus	Thymus
34	chr19:41121200-41125200	Weak transcription	Spleen	Spleen
35	chr19:41121200-41125200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr19:41121200-41125800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr19:41121200-41129400	Weak transcription	Right Atrium	heart
38	chr19:41121200-41136400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr19:41121200-41137400	Strong transcription	Fetal Muscle Leg	muscle
40	chr19:41121400-41125000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr19:41121400-41125000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr19:41121400-41125000	Weak transcription	Fetal Kidney	kidney
43	chr19:41121400-41125200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr19:41121400-41125200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:41121400-41125200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr19:41121400-41125200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr19:41121400-41125200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:41121400-41125200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:41121400-41125400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:41121400-41125400	Weak transcription	GM12878-XiMat	blood

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