Variant report

Variant	rs11083475
Chromosome Location	chr19:39188112-39188113
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	MYC	chr19:39187869-39188159	MCF10A-Er-Src	breast:	n/a	chr19:39187978-39187993 chr19:39187981-39187992 chr19:39187982-39187991 chr19:39187980-39187995
2	POLR2A	chr19:39187878-39188799	U87	brain:	n/a	n/a
3	POLR2A	chr19:39187972-39189382	A549	lung:	n/a	n/a
4	FOS	chr19:39187872-39188142	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr19:39187884-39188798	U87	brain:	n/a	n/a
6	POLR2A	chr19:39164600-39206677	PANC-1	pancreas:	n/a	n/a
7	FOS	chr19:39187869-39188128	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr19:39187886-39188149	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr19:39164601-39206634	PANC-1	pancreas:	n/a	n/a
10	MYC	chr19:39187871-39188173	MCF10A-Er-Src	breast:	n/a	chr19:39187978-39187993 chr19:39187981-39187992 chr19:39187982-39187991 chr19:39187980-39187995

No.	Distal block	Cell Line	Cell type
1	chr19:39147345..39151436-chr19:39186794..39189528,4	MCF-7	breast:
2	chr19:39188109..39192959-chr19:39197820..39200400,6	MCF-7	breast:
3	chr19:39135966..39142009-chr19:39184894..39201240,23	MCF-7	breast:
4	chr19:39182129..39185762-chr19:39186877..39189539,4	MCF-7	breast:
5	chr19:39176509..39181573-chr19:39186750..39192510,7	K562	blood:
6	chr19:39173031..39174983-chr19:39187946..39191555,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267375	TF binding region
ENSG00000130402	Chromatin interaction
ENSG00000267375	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10403540	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10406778	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10415219	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10415646	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10421560	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10426809	0.80[JPT][hapmap];0.88[YRI][hapmap]
rs12460849	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12462270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13343794	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13344413	0.92[CEU][hapmap]
rs16972767	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2279144	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2303040	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs28488032	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28624276	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3745859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3786835	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3786837	0.88[EUR][1000 genomes]
rs3786839	1.00[CEU][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes]
rs3786845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3786848	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3786851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3810341	0.81[ASN][1000 genomes]
rs55876653	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55945853	0.86[EUR][1000 genomes]
rs56113315	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56365761	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62120083	0.86[EUR][1000 genomes]
rs62121814	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62121816	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62121818	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7251903	1.00[CEU][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes]
rs7252589	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7254100	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107416	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs8111746	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs883394	0.95[EUR][1000 genomes]
rs883433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs979971	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs979972	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Heart rate	23583979	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
2	chr19:39177200-39195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:39178600-39190600	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr19:39178600-39198200	Genic enhancers	Fetal Intestine Large	intestine
5	chr19:39179000-39189400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:39179600-39205800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr19:39180000-39191600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:39180000-39192400	Genic enhancers	Lung	lung
9	chr19:39182000-39194200	Genic enhancers	Fetal Muscle Leg	muscle
10	chr19:39182200-39192600	Enhancers	Liver	Liver
11	chr19:39182200-39193400	Enhancers	Right Atrium	heart
12	chr19:39182200-39193800	Genic enhancers	Fetal Stomach	stomach
13	chr19:39182200-39214200	Genic enhancers	Fetal Muscle Trunk	muscle
14	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr19:39182400-39189600	Enhancers	Brain Angular Gyrus	brain
16	chr19:39182400-39193600	Genic enhancers	Esophagus	oesophagus
17	chr19:39182600-39190200	Genic enhancers	Colonic Mucosa	Colon
18	chr19:39182600-39190800	Genic enhancers	HepG2	liver
19	chr19:39182600-39193800	Genic enhancers	Rectal Mucosa Donor 31	rectum
20	chr19:39183000-39190000	Enhancers	Brain Cingulate Gyrus	brain
21	chr19:39183000-39196600	Enhancers	Fetal Heart	heart
22	chr19:39183200-39188800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
23	chr19:39183400-39191000	Genic enhancers	Placenta	Placenta
24	chr19:39183800-39188200	Weak transcription	Fetal Brain Female	brain
25	chr19:39184400-39189200	Weak transcription	Brain Germinal Matrix	brain
26	chr19:39184400-39190200	Enhancers	Brain Anterior Caudate	brain
27	chr19:39184400-39191200	Enhancers	Brain Hippocampus Middle	brain
28	chr19:39184600-39188800	Genic enhancers	NHEK	skin
29	chr19:39184800-39188200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:39184800-39188600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:39184800-39188600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr19:39184800-39188600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:39184800-39188800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr19:39184800-39189600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:39184800-39190000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:39184800-39190400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr19:39184800-39190800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:39184800-39205800	Genic enhancers	A549	lung
39	chr19:39185000-39188200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:39185000-39193600	Genic enhancers	HSMM	muscle
41	chr19:39185200-39188200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:39185200-39188400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:39185200-39188400	Strong transcription	Dnd41	blood
44	chr19:39185200-39205800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:39185400-39192000	Strong transcription	Osteobl	bone
46	chr19:39185600-39189000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:39185800-39189600	Enhancers	Brain Substantia Nigra	brain
48	chr19:39185800-39189800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:39185800-39190000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr19:39185800-39190000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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