Variant report

Variant	rs61736260
Chromosome Location	chr19:39860299-39860300
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	chr19:39850716-39886400	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39860188-39860480	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39859941..39863633-chr19:39878903..39882994,5	MCF-7	breast:
2	chr19:39843827..39847459-chr19:39858082..39862141,4	MCF-7	breast:
3	chr19:39859164..39862677-chr19:39900156..39904174,3	MCF-7	breast:

Variant related genes	Relation type
SAMD4B	TF binding region
ENSG00000063322	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000266559	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs40469	0.82[EUR][1000 genomes]
rs45591338	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs45613331	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62119672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62119675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62119723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62122887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62122888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62122889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62122891	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62122892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:39835800-39880200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:39835800-39880200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr19:39836200-39880400	Strong transcription	Primary T cells from cord blood	blood
5	chr19:39836400-39862600	Strong transcription	Duodenum Mucosa	Duodenum
6	chr19:39836600-39864000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr19:39836600-39880400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr19:39836600-39880400	Strong transcription	Fetal Brain Female	brain
9	chr19:39837400-39880000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr19:39837600-39863600	Strong transcription	Fetal Intestine Small	intestine
11	chr19:39838000-39880000	Strong transcription	Brain Germinal Matrix	brain
12	chr19:39838200-39862600	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr19:39838600-39880400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr19:39838800-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:39839200-39879200	Strong transcription	Dnd41	blood
16	chr19:39841600-39880000	Strong transcription	Fetal Intestine Large	intestine
17	chr19:39842000-39864200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr19:39842000-39880000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr19:39842200-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:39842200-39880400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr19:39842400-39862400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:39842400-39880400	Strong transcription	Thymus	Thymus
23	chr19:39842600-39880400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:39847400-39864000	Strong transcription	Primary hematopoietic stem cells	blood
25	chr19:39848200-39880000	Weak transcription	Fetal Heart	heart
26	chr19:39848400-39864200	Strong transcription	K562	blood
27	chr19:39850400-39881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr19:39851400-39861000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr19:39851600-39862800	Weak transcription	Small Intestine	intestine
30	chr19:39851600-39866400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr19:39851800-39860800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr19:39851800-39867600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr19:39852800-39880400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr19:39853600-39863000	Strong transcription	A549	lung
35	chr19:39853800-39862800	Weak transcription	Right Atrium	heart
36	chr19:39854000-39860400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:39854000-39866200	Weak transcription	Stomach Mucosa	stomach
38	chr19:39854000-39876000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:39854600-39862400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:39854800-39861600	Strong transcription	Placenta	Placenta
41	chr19:39854800-39862200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:39855000-39861200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr19:39855000-39862400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr19:39855000-39865600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:39855200-39862600	Strong transcription	HSMM	muscle
46	chr19:39855400-39862600	Strong transcription	Fetal Stomach	stomach
47	chr19:39855600-39861000	Weak transcription	GM12878-XiMat	blood
48	chr19:39855600-39862600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:39855600-39862600	Strong transcription	Adipose Nuclei	Adipose
50	chr19:39855600-39862800	Strong transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links