Variant report

Variant	rs1105759
Chromosome Location	chr19:39217507-39217508
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	MAX	chr19:39217408-39217664	K562	blood:	n/a	chr19:39217529-39217545
2	POLR2A	chr19:39216993-39217648	K562	blood:	n/a	n/a
3	POLR2A	chr19:39217284-39218248	A549	lung:	n/a	n/a
4	POLR2A	chr19:39217418-39217854	MCF-7	breast:	n/a	n/a
5	POLR2A	chr19:39217091-39217764	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:39217457-39218094	HepG2	liver:	n/a	n/a
7	TCF12	chr19:39216992-39218065	A549	lung:	n/a	chr19:39217138-39217148 chr19:39217867-39217877
8	POLR2A	chr19:39217188-39217788	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:39217320-39217776	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:39216954-39218717	K562	blood:	n/a	n/a
11	POLR2A	chr19:39217331-39218030	A549	lung:	n/a	n/a
12	ZNF263	chr19:39217297-39217879	HEK293-T-REx	kidney:	n/a	n/a
13	POLR2A	chr19:39217329-39217931	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr19:39217503-39217741	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:39217344-39218937	Hela-S3	cervix:	n/a	n/a
16	FOSL2	chr19:39217442-39217771	HepG2	liver:	n/a	n/a
17	POLR2A	chr19:39217350-39217730	A549	lung:	n/a	n/a
18	POLR2A	chr19:39216839-39218116	K562	blood:	n/a	n/a
19	POLR2A	chr19:39206681-39226302	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr19:39216964-39218967	A549	lung:	n/a	n/a
21	EGR1	chr19:39217420-39217722	K562	blood:	n/a	chr19:39217577-39217586
22	POLR2A	chr19:39216942-39217820	K562	blood:	n/a	n/a
23	POLR2A	chr19:39217280-39217540	HCT-116	colon:	n/a	n/a
24	POLR2A	chr19:39217303-39218059	HL-60	blood:	n/a	n/a
25	BCL3	chr19:39217061-39218088	A549	lung:	n/a	chr19:39217491-39217500 chr19:39217120-39217133
26	POLR2A	chr19:39217334-39217829	GM12878	blood:	n/a	n/a
27	BCL3	chr19:39216937-39217765	A549	lung:	n/a	chr19:39217491-39217500 chr19:39217120-39217133
28	E2F6	chr19:39217434-39217562	K562	blood:	n/a	chr19:39217501-39217513
29	POLR2A	chr19:39217443-39217702	HepG2	liver:	n/a	n/a
30	POLR2A	chr19:39217261-39217629	GM12891	blood:	n/a	n/a
31	POLR2A	chr19:39217482-39217648	ProgFib	skin:	n/a	n/a
32	POLR2A	chr19:39217311-39218012	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:39216916-39217910	HepG2	liver:	n/a	n/a
34	SIN3AK20	chr19:39216976-39218202	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr19:39217280-39217878	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr19:39217385-39217797	GM12891	blood:	n/a	n/a
37	POLR2A	chr19:39206712-39220782	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr19:39217396-39217598	HepG2	liver:	n/a	n/a
39	POLR2A	chr19:39216946-39218155	K562	blood:	n/a	n/a
40	EGR1	chr19:39217389-39217691	K562	blood:	n/a	chr19:39217577-39217586

No.	Distal block	Cell Line	Cell type
1	chr19:39215761..39217531-chr19:39221029..39224006,3	MCF-7	breast:
2	chr19:39217331..39220252-chr19:39336372..39338597,2	K562	blood:
3	chr19:39216544..39219007-chr19:39328306..39331285,2	MCF-7	breast:
4	chr19:39201322..39204125-chr19:39215978..39220088,5	K562	blood:
5	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
6	chr19:39138000..39140768-chr19:39215687..39223350,9	MCF-7	breast:

Variant related genes	Relation type
ACTN4	TF binding region
ENSG00000104824	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1136956	0.86[ASN][1000 genomes]
rs12974733	0.89[ASN][1000 genomes]
rs12975079	0.89[ASN][1000 genomes]
rs12975256	0.83[ASN][1000 genomes]
rs12978715	0.89[ASN][1000 genomes]
rs12979947	0.89[ASN][1000 genomes]
rs12980399	0.86[ASN][1000 genomes]
rs12981131	0.89[ASN][1000 genomes]
rs12984794	0.83[ASN][1000 genomes]
rs12985558	0.89[ASN][1000 genomes]
rs12986032	0.82[AMR][1000 genomes]
rs12986337	0.89[ASN][1000 genomes]
rs2086148	0.89[ASN][1000 genomes]
rs2126970	0.89[ASN][1000 genomes]
rs2279145	0.83[ASN][1000 genomes]
rs2279146	0.83[ASN][1000 genomes]
rs34026184	0.89[ASN][1000 genomes]
rs34082501	0.83[ASN][1000 genomes]
rs34134906	0.89[ASN][1000 genomes]
rs34563817	0.89[ASN][1000 genomes]
rs34703567	0.89[ASN][1000 genomes]
rs34717167	0.89[ASN][1000 genomes]
rs35281901	0.89[ASN][1000 genomes]
rs35640008	0.83[ASN][1000 genomes]
rs35666464	0.86[ASN][1000 genomes]
rs35729716	0.83[ASN][1000 genomes]
rs35807146	0.81[ASN][1000 genomes]
rs35856174	0.83[ASN][1000 genomes]
rs45599933	0.81[ASN][1000 genomes]
rs62119115	0.86[ASN][1000 genomes]
rs62119116	0.89[ASN][1000 genomes]
rs62120068	0.89[ASN][1000 genomes]
rs62120072	0.81[ASN][1000 genomes]
rs62120074	0.83[ASN][1000 genomes]
rs71356822	0.89[ASN][1000 genomes]
rs7248577	0.89[ASN][1000 genomes]
rs8104815	0.83[ASN][1000 genomes]
rs8105055	0.83[ASN][1000 genomes]
rs8105069	0.83[ASN][1000 genomes]
rs8105216	0.83[ASN][1000 genomes]
rs8105550	0.83[ASN][1000 genomes]
rs899199	0.83[ASN][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	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
6	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
7	nsv911669	chr19:39196745-39231548	Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 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	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39189400-39223400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:39189800-39222800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:39190000-39218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:39190200-39222600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr19:39190200-39222800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr19:39190400-39218000	Strong transcription	Primary T cells from cord blood	blood
8	chr19:39190400-39222400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:39190400-39222600	Strong transcription	Dnd41	blood
10	chr19:39190600-39219600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:39190600-39222800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:39190800-39220400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr19:39190800-39222600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr19:39190800-39222600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:39190800-39222800	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr19:39190800-39223000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr19:39190800-39223000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:39191000-39222400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr19:39191000-39222600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr19:39191400-39218800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:39192400-39221200	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr19:39199000-39220400	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr19:39202800-39221400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr19:39203400-39218600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:39204200-39223400	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr19:39205000-39221000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr19:39206800-39220000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:39206800-39220000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:39207000-39219400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr19:39207000-39220200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:39207000-39222400	Strong transcription	Fetal Brain Female	brain
32	chr19:39210000-39218400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr19:39210200-39222600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:39210400-39223400	Strong transcription	NHLF	lung
35	chr19:39210400-39223400	Strong transcription	Osteobl	bone
36	chr19:39210600-39219000	Strong transcription	Rectal Smooth Muscle	rectum
37	chr19:39210600-39222000	Strong transcription	Small Intestine	intestine
38	chr19:39210600-39222800	Genic enhancers	Spleen	Spleen
39	chr19:39210800-39219200	Strong transcription	NHEK	skin
40	chr19:39210800-39220200	Strong transcription	Thymus	Thymus
41	chr19:39211000-39218800	Strong transcription	Pancreatic Islets	Pancreatic Islet
42	chr19:39211000-39220800	Strong transcription	Colon Smooth Muscle	Colon
43	chr19:39211200-39218000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:39211200-39218600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:39211200-39218600	Weak transcription	Fetal Brain Male	brain
46	chr19:39211200-39219800	Strong transcription	Fetal Lung	lung
47	chr19:39211200-39220000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:39211200-39221400	Strong transcription	Esophagus	oesophagus
49	chr19:39211200-39222000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:39211200-39224000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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