Variant report

Variant	rs61486503
Chromosome Location	chr19:39107156-39107157
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr19:39106900-39107308	GM12878	blood:	n/a	n/a
2	ELK1	chr19:39107118-39107316	GM12878	blood:	n/a	n/a
3	ZNF143	chr19:39106974-39107253	GM12878	blood:	n/a	n/a
4	YY1	chr19:39106995-39107236	GM12878	blood:	n/a	n/a
5	EBF1	chr19:39106989-39107222	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:39107089-39107275	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:39106842-39107374	GM12892	blood:	n/a	n/a
8	IKZF1	chr19:39106873-39107382	GM12878	blood:	n/a	n/a
9	SPI1	chr19:39106979-39107181	GM12891	blood:	n/a	n/a
10	POLR2A	chr19:39106887-39107538	GM12891	blood:	n/a	n/a
11	RUNX3	chr19:39106870-39107268	GM12878	blood:	n/a	n/a
12	ELF1	chr19:39107000-39107271	GM12878	blood:	n/a	n/a
13	ATF2	chr19:39106816-39107261	GM12878	blood:	n/a	n/a
14	MAX	chr19:39107093-39107198	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:39107075-39107195	GM12878	blood:	n/a	n/a
16	MTA3	chr19:39106885-39107671	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:39106960-39107415	GM12878	blood:	n/a	n/a
18	WRNIP1	chr19:39106942-39107583	GM12878	blood:	n/a	n/a
19	FOXM1	chr19:39106949-39107228	GM12878	blood:	n/a	n/a
20	RUNX3	chr19:39106896-39107198	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:39107084-39107306	GM12878	blood:	n/a	n/a
22	CTCF	chr19:39107040-39107190	GM12865	blood:	n/a	n/a
23	POLR2A	chr19:39107052-39107264	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39106830..39111691-chr19:39117375..39123240,7	MCF-7	breast:
2	chr19:39086098..39088583-chr19:39106611..39110096,5	K562	blood:
3	chr19:39103433..39106687-chr19:39106977..39109796,8	K562	blood:
4	chr19:39105818..39107415-chr19:39115020..39117364,2	K562	blood:
5	chr19:39104481..39107303-chr19:39137807..39140302,2	K562	blood:
6	chr19:39103495..39106423-chr19:39106849..39111061,4	MCF-7	breast:
7	chr19:39101758..39105983-chr19:39106668..39109959,5	K562	blood:

No data

Variant related genes	Relation type
EIF3K	TF binding region
MAP4K1	TF binding region
ENSG00000178982	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000267291	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16972761	0.85[EUR][1000 genomes]
rs2232991	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58441402	0.93[EUR][1000 genomes]
rs58964344	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6508811	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	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
6	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

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39087200-39107800	Weak transcription	Colonic Mucosa	Colon
2	chr19:39087400-39107400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr19:39087400-39108200	Weak transcription	Gastric	stomach
4	chr19:39087400-39108800	Weak transcription	Right Atrium	heart
5	chr19:39092600-39109000	Weak transcription	Small Intestine	intestine
6	chr19:39096800-39108000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:39097800-39108200	Weak transcription	Fetal Intestine Small	intestine
8	chr19:39098600-39108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:39102000-39108600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:39102200-39107200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:39102200-39107400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr19:39103600-39107400	Weak transcription	Fetal Thymus	thymus
13	chr19:39103600-39108000	Weak transcription	Lung	lung
14	chr19:39103600-39108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:39104200-39107200	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr19:39104400-39107200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:39104400-39107200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:39104800-39108600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:39105200-39107800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr19:39106000-39107200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr19:39106000-39107200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:39106200-39107200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr19:39106200-39108600	Weak transcription	A549	lung
24	chr19:39106200-39108600	Weak transcription	HepG2	liver
25	chr19:39106200-39108800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:39106400-39107200	Enhancers	Primary B cells from cord blood	blood
27	chr19:39106400-39107800	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr19:39106400-39108200	Weak transcription	K562	blood
29	chr19:39106600-39108200	Weak transcription	Placenta	Placenta
30	chr19:39106800-39107200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
31	chr19:39106800-39107200	Flanking Active TSS	GM12878-XiMat	blood
32	chr19:39106800-39107400	Enhancers	Primary T cells from cord blood	blood
33	chr19:39106800-39107800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr19:39106800-39107800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:39106800-39108000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr19:39106800-39108000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:39106800-39109600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr19:39107000-39107200	Weak transcription	Thymus	Thymus
39	chr19:39107000-39107400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:39107000-39107400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr19:39107000-39107600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:39107000-39107600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr19:39107000-39108000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:39107000-39108000	Enhancers	Spleen	Spleen
45	chr19:39107000-39109200	Flanking Active TSS	Dnd41	blood
46	chr19:39107000-39109400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr19:39107000-39109600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links