Variant report

Variant	rs73038948
Chromosome Location	chr19:39228244-39228245
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr19:39227076-39228452	H1-hESC	embryonic stem cell:	n/a	chr19:39227759-39227770
2	MAX	chr19:39226613-39228363	A549	lung:	n/a	n/a
3	E2F6	chr19:39227980-39228265	K562	blood:	n/a	n/a
4	MAX	chr19:39227544-39228476	HepG2	liver:	n/a	n/a
5	MAX	chr19:39227360-39228404	HepG2	liver:	n/a	n/a
6	E2F6	chr19:39227639-39228287	K562	blood:	n/a	chr19:39227759-39227770
7	HMGN3	chr19:39228067-39228337	K562	blood:	n/a	n/a
8	SPI1	chr19:39228162-39228341	K562	blood:	n/a	n/a
9	POLR2A	chr19:39228191-39228251	K562	blood:	n/a	n/a
10	ELF1	chr19:39227933-39228460	GM12878	blood:	n/a	chr19:39228333-39228344 chr19:39228333-39228344
11	TCF12	chr19:39228042-39228728	A549	lung:	n/a	n/a
12	MAX	chr19:39227567-39228347	K562	blood:	n/a	n/a
13	E2F6	chr19:39227512-39228307	H1-hESC	embryonic stem cell:	n/a	chr19:39227759-39227770
14	POLR2A	chr19:39227653-39231282	PANC-1	pancreas:	n/a	n/a
15	ZBTB7A	chr19:39226587-39228377	K562	blood:	n/a	chr19:39227221-39227228
16	CEBPB	chr19:39228153-39228353	K562	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39227687..39231006-chr19:39233180..39235814,6	K562	blood:
2	chr19:39218553..39228703-chr19:39324875..39331730,17	MCF-7	breast:
3	chr19:39225035..39229236-chr19:39320225..39324035,5	K562	blood:
4	chr19:39226181..39228990-chr19:39419347..39420876,2	K562	blood:
5	chr19:39136334..39138370-chr19:39226702..39229509,2	MCF-7	breast:
6	chr19:39226722..39228357-chr19:39340194..39343791,3	K562	blood:
7	chr19:39227434..39229644-chr19:39233125..39236145,3	MCF-7	breast:
8	chr19:39226378..39228332-chr19:39339696..39342519,3	K562	blood:
9	chr19:39220252..39229073-chr19:39338371..39342954,10	MCF-7	breast:
10	chr19:39225241..39228879-chr19:39342547..39344492,3	K562	blood:
11	chr19:39224374..39227247-chr19:39227661..39229256,2	MCF-7	breast:
12	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
13	chr19:39226859..39228990-chr19:39419347..39420977,2	K562	blood:
14	chr19:39223964..39228282-chr19:39327392..39332302,8	MCF-7	breast:
15	chr19:39138420..39142103-chr19:39224990..39229224,5	MCF-7	breast:
16	chr19:39221972..39229243-chr19:39319630..39326763,11	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACTN4-1	chr19:39227984-39229819	NONHSAT066238

No data

Variant related genes	Relation type
ENSG00000267892	TF binding region
CAPN12	TF binding region
ENSG00000130402	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000182472	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11553600	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052046	1.00[ASN][1000 genomes]
rs17589415	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17665451	1.00[ASN][1000 genomes]
rs41482151	1.00[ASN][1000 genomes]
rs45468197	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616403	1.00[ASN][1000 genomes]
rs4802744	1.00[ASN][1000 genomes]
rs4802747	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802775	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67438539	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67953948	1.00[ASN][1000 genomes]
rs7258742	1.00[ASN][1000 genomes]
rs73032668	1.00[ASN][1000 genomes]
rs73032691	1.00[ASN][1000 genomes]
rs73032697	1.00[ASN][1000 genomes]
rs73034621	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038909	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038918	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038924	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038930	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038932	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73038936	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7351086	1.00[ASN][1000 genomes]
rs7507890	0.85[AMR][1000 genomes]
rs8103824	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8182484	1.00[ASN][1000 genomes]
rs888995	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
8	esv3421629	chr19:39225537-39228485	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3360199	chr19:39225562-39228860	Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv3437673	chr19:39225662-39228610	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39226000-39228400	Enhancers	Placenta	Placenta
2	chr19:39226000-39229200	Weak transcription	Gastric	stomach
3	chr19:39226200-39228400	Enhancers	GM12878-XiMat	blood
4	chr19:39226200-39228600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:39226200-39228600	Enhancers	Spleen	Spleen
6	chr19:39226200-39230200	Weak transcription	NHEK	skin
7	chr19:39226200-39230600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:39226600-39228400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:39226800-39228600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:39227000-39232200	Weak transcription	Left Ventricle	heart
11	chr19:39227200-39228400	Enhancers	Fetal Lung	lung
12	chr19:39227400-39228400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr19:39227400-39228400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:39227400-39234600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:39227600-39228400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:39227600-39228400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:39227600-39228400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr19:39227600-39228400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr19:39227600-39228400	Enhancers	Primary B cells from cord blood	blood
20	chr19:39227600-39228600	Enhancers	Fetal Intestine Large	intestine
21	chr19:39227600-39228600	Enhancers	A549	lung
22	chr19:39227600-39229000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:39227600-39229800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:39227600-39231200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:39227800-39228600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
26	chr19:39228000-39228400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr19:39228000-39228400	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr19:39228000-39228400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr19:39228000-39228400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:39228000-39228400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
31	chr19:39228000-39228400	Flanking Active TSS	HepG2	liver
32	chr19:39228000-39228600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:39228000-39228600	Flanking Active TSS	K562	blood
34	chr19:39228000-39229400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:39228000-39231000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:39228000-39231000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr19:39228000-39231600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr19:39228200-39228400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
39	chr19:39228200-39228400	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr19:39228200-39228400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr19:39228200-39228400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:39228200-39228400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:39228200-39228400	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
44	chr19:39228200-39228600	Enhancers	Primary hematopoietic stem cells	blood
45	chr19:39228200-39228600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:39228200-39229000	Weak transcription	Esophagus	oesophagus
47	chr19:39228200-39229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:39228200-39229600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr19:39228200-39229600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr19:39228200-39230200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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