Variant report

Variant	rs12609803
Chromosome Location	chr19:36232875-36232876
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	chr19:36227197-36234067	GM12891	blood:	n/a	n/a
2	POLR2A	chr19:36232497-36234060	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:36232806-36234125	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:36227116-36234243	GM12878	blood:	n/a	n/a
5	MTA3	chr19:36232868-36234042	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:36232860-36234120	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:36228209-36234132	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36205476..36213390-chr19:36226310..36233646,27	MCF-7	breast:
2	chr19:36231491..36233720-chr19:36248400..36250494,2	MCF-7	breast:
3	chr19:36231818..36233362-chr19:36425701..36428426,2	MCF-7	breast:

Variant related genes	Relation type
PSENEN	TF binding region
ENSG00000188223	TF binding region
IGFLR1	TF binding region
ENSG00000126243	Chromatin interaction
ENSG00000167595	Chromatin interaction
ENSG00000272333	Chromatin interaction
ENSG00000004776	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs107878	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11084828	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11667696	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670414	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11671520	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11672164	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12151356	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17776911	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3746278	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787051	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3848663	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3885794	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3885795	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4806197	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4806198	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4806201	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4806202	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58561864	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66747537	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv515536	chr19:36219525-36240960	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36230600-36233200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr19:36230800-36233000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr19:36230800-36234000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr19:36230800-36234000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
5	chr19:36230800-36234000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr19:36230800-36234000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:36230800-36234000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:36230800-36234200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr19:36230800-36234400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr19:36231000-36233200	Active TSS	Rectal Smooth Muscle	rectum
11	chr19:36231000-36234000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr19:36231200-36233000	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr19:36231200-36233800	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr19:36231400-36235200	Weak transcription	Fetal Heart	heart
15	chr19:36231800-36234000	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr19:36231800-36234000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:36231800-36234200	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr19:36232000-36234800	Weak transcription	Gastric	stomach
19	chr19:36232200-36233000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr19:36232200-36233000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:36232200-36233000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:36232200-36233000	Weak transcription	Brain Hippocampus Middle	brain
23	chr19:36232200-36233000	Weak transcription	Colonic Mucosa	Colon
24	chr19:36232200-36233000	Weak transcription	Colon Smooth Muscle	Colon
25	chr19:36232200-36233000	Weak transcription	Fetal Stomach	stomach
26	chr19:36232200-36233000	Weak transcription	A549	lung
27	chr19:36232200-36233000	Weak transcription	NHEK	skin
28	chr19:36232200-36233200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:36232200-36233200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:36232200-36233200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:36232200-36233200	Weak transcription	Brain Angular Gyrus	brain
32	chr19:36232200-36233200	Weak transcription	Brain Anterior Caudate	brain
33	chr19:36232200-36233200	Weak transcription	Brain Substantia Nigra	brain
34	chr19:36232200-36233200	Weak transcription	Esophagus	oesophagus
35	chr19:36232200-36233200	Weak transcription	Fetal Intestine Large	intestine
36	chr19:36232200-36233200	Weak transcription	Left Ventricle	heart
37	chr19:36232200-36233200	Weak transcription	Lung	lung
38	chr19:36232200-36233200	Enhancers	Spleen	Spleen
39	chr19:36232200-36233400	Weak transcription	Fetal Lung	lung
40	chr19:36232200-36233800	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr19:36232200-36234000	Active TSS	Duodenum Mucosa	Duodenum
42	chr19:36232200-36234800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:36232200-36234800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:36232200-36234800	Weak transcription	Fetal Kidney	kidney
45	chr19:36232200-36234800	Weak transcription	Right Ventricle	heart
46	chr19:36232200-36234800	Weak transcription	Hela-S3	cervix
47	chr19:36232200-36235000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:36232200-36235000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:36232200-36235000	Weak transcription	Fetal Brain Male	brain
50	chr19:36232200-36235000	Weak transcription	Stomach Mucosa	stomach

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