Variant report

Variant	rs60759642
Chromosome Location	chr19:38851822-38851823
allele	A/C
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	TCF12	chr19:38850909-38853674	A549	lung:	n/a	chr19:38852144-38852154
2	BCL3	chr19:38851416-38853478	A549	lung:	n/a	chr19:38852942-38852951
3	RCOR1	chr19:38851617-38851888	K562	blood:	n/a	n/a
4	ZNF263	chr19:38851732-38852408	K562	blood:	n/a	n/a
5	RCOR1	chr19:38851499-38853495	K562	blood:	n/a	n/a
6	ZNF143	chr19:38851562-38851825	K562	blood:	n/a	n/a
7	ZNF263	chr19:38851579-38852538	HEK293-T-REx	kidney:	n/a	n/a
8	MAX	chr19:38851469-38853707	A549	lung:	n/a	chr19:38851906-38851913 chr19:38852622-38852632
9	GATA2	chr19:38851789-38852232	K562	blood:	n/a	chr19:38852033-38852043 chr19:38852035-38852042 chr19:38852035-38852042 chr19:38852035-38852042 chr19:38852028-38852049 chr19:38852033-38852042 chr19:38852030-38852046

No.	Distal block	Cell Line	Cell type
1	chr19:38843850..38848913-chr19:38849820..38852865,6	K562	blood:
2	chr19:38851531..38855576-chr19:38863499..38866575,5	MCF-7	breast:
3	chr19:38745341..38747261-chr19:38850863..38853246,2	K562	blood:
4	chr19:38851019..38853857-chr19:38863435..38867110,13	MCF-7	breast:
5	chr19:38851103..38853998-chr19:38877778..38880419,3	K562	blood:
6	chr19:38850348..38855103-chr19:38862504..38867180,11	K562	blood:
7	chr19:38755112..38757929-chr19:38851639..38853560,2	MCF-7	breast:
8	chr19:38826255..38829380-chr19:38850634..38854376,3	MCF-7	breast:
9	chr19:38851022..38852568-chr5:122434797..122437026,2	MCF-7	breast:
10	chr19:36629391..36631341-chr19:38851035..38853209,2	MCF-7	breast:
11	chr19:38849999..38854779-chr19:38863669..38868606,10	K562	blood:
12	chr19:38831821..38834669-chr19:38850986..38853085,2	MCF-7	breast:
13	chr19:38846299..38848988-chr19:38850348..38854198,4	MCF-7	breast:
14	chr19:38845897..38848818-chr19:38850039..38852720,3	K562	blood:
15	chr19:38718872..38720876-chr19:38850703..38853087,2	MCF-7	breast:

Variant related genes	Relation type
CATSPERG	TF binding region
ENSG00000167642	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000167641	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000061455	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000099338	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1060455	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11083453	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12460181	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12460264	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12460599	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12461248	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12461700	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12462230	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12463175	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072350	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2074979	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2074980	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2286547	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2286550	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286551	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2302226	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35848839	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3745955	0.91[ASN][1000 genomes]
rs3745956	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3745960	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3745961	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3745962	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60577771	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60915799	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61379500	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	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

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38828200-38852000	Weak transcription	Right Atrium	heart
2	chr19:38835200-38852000	Weak transcription	Pancreas	Pancrea
3	chr19:38851000-38852400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr19:38851400-38852000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr19:38851400-38852000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:38851400-38853400	Active TSS	Hela-S3	cervix
7	chr19:38851600-38852000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:38851600-38852000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:38851600-38852000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr19:38851800-38852000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:38851800-38852000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr19:38851800-38852000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
13	chr19:38851800-38852000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
14	chr19:38851800-38852000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr19:38851800-38852000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr19:38851800-38852000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:38851800-38852000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:38851800-38852000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:38851800-38852000	Bivalent Enhancer	Adipose Nuclei	Adipose
20	chr19:38851800-38852000	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:38851800-38852000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
22	chr19:38851800-38852000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr19:38851800-38852000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr19:38851800-38852000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
25	chr19:38851800-38852000	Enhancers	Right Ventricle	heart
26	chr19:38851800-38852000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
27	chr19:38851800-38852000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
28	chr19:38851800-38852000	Bivalent Enhancer	HMEC	breast
29	chr19:38851800-38852000	Bivalent Enhancer	NHEK	skin
30	chr19:38851800-38852200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:38851800-38852200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:38851800-38852200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr19:38851800-38852200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:38851800-38852200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:38851800-38852200	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:38851800-38852200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:38851800-38852200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:38851800-38852200	Bivalent Enhancer	Fetal Intestine Small	intestine
39	chr19:38851800-38852200	Bivalent Enhancer	Placenta	Placenta
40	chr19:38851800-38852200	Enhancers	Lung	lung
41	chr19:38851800-38852200	Flanking Bivalent TSS/Enh	A549	lung
42	chr19:38851800-38852200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
43	chr19:38851800-38852400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr19:38851800-38852400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr19:38851800-38852400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
46	chr19:38851800-38852400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr19:38851800-38852400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:38851800-38852400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
49	chr19:38851800-38852400	Enhancers	Spleen	Spleen
50	chr19:38851800-38852400	Flanking Active TSS	K562	blood

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