Variant report

Variant	rs2073900
Chromosome Location	chr19:35741456-35741457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HMGN3	chr19:35741344-35741531	K562	blood:	n/a	n/a
2	POLR2A	chr19:35740916-35741591	MCF-7	breast:	n/a	n/a
3	POLR2A	chr19:35741133-35741500	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr19:35741392-35741593	MCF-7	breast:	n/a	n/a
5	POLR2A	chr19:35738375-35741593	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:35740827-35741610	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:35740917-35741627	HepG2	liver:	n/a	n/a
8	POLR2A	chr19:35737830-35741820	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35644198..35645864-chr19:35739143..35741806,2	MCF-7	breast:
2	chr19:35654052..35658593-chr19:35736953..35742683,9	K562	blood:
3	chr19:35627197..35629853-chr19:35739578..35741955,2	K562	blood:
4	chr19:35639021..35648956-chr19:35737438..35742195,14	K562	blood:
5	chr19:35739927..35742259-chr19:35996033..35997931,2	K562	blood:
6	chr19:35625494..35628326-chr19:35738306..35742693,4	MCF-7	breast:
7	chr19:35519110..35522906-chr19:35737918..35741487,5	MCF-7	breast:
8	chr19:35644753..35650464-chr19:35737058..35742117,12	K562	blood:
9	chr19:35603872..35607710-chr19:35737437..35742074,6	MCF-7	breast:
10	chr19:35631922..35638346-chr19:35737284..35742337,12	MCF-7	breast:
11	chr19:35739560..35741618-chr19:36133175..36135201,2	K562	blood:
12	chr19:35630586..35637861-chr19:35737374..35742554,18	MCF-7	breast:

No data

Variant related genes	Relation type
LSR	TF binding region
ENSG00000105711	Chromatin interaction
ENSG00000221946	Chromatin interaction
ENSG00000105672	Chromatin interaction
ENSG00000089356	Chromatin interaction
ENSG00000089327	Chromatin interaction
ENSG00000221857	Chromatin interaction
ENSG00000266964	Chromatin interaction
ENSG00000161249	Chromatin interaction
ENSG00000153902	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10416254	0.82[JPT][hapmap]
rs10418562	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs10421791	0.80[YRI][hapmap]
rs10422195	0.82[JPT][hapmap]
rs11669258	0.82[JPT][hapmap]
rs12609790	0.81[ASN][1000 genomes]
rs2188327	0.84[ASN][1000 genomes]
rs2861485	0.80[YRI][hapmap]
rs2861487	0.84[ASN][1000 genomes]
rs2861488	0.84[ASN][1000 genomes]
rs34926220	0.85[ASN][1000 genomes]
rs4806117	0.82[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4806119	0.80[YRI][hapmap]
rs534706	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6510474	0.85[ASN][1000 genomes]
rs7248460	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7249852	0.85[ASN][1000 genomes]
rs7249941	0.85[ASN][1000 genomes]
rs7249962	0.85[ASN][1000 genomes]
rs7250531	0.85[ASN][1000 genomes]
rs7253876	0.85[ASN][1000 genomes]
rs7255786	0.84[ASN][1000 genomes]
rs7256604	0.84[ASN][1000 genomes]
rs8112032	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.83[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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv1066553	chr19:35698638-35749563	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	nsv978896	chr19:35724047-35748472	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv911618	chr19:35734107-35807845	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
10	esv1836312	chr19:35741456-35786868	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2073900	FCGBP	cis	cerebellum	SCAN
rs2073900	ENSG00000105699	cis	multi-tissue	Pritchard
rs2073900	ZNF793	cis	cerebellum	SCAN
rs2073900	NFKBIB	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35740400-35744600	Weak transcription	Left Ventricle	heart
2	chr19:35740600-35741600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr19:35740600-35745200	Weak transcription	Right Atrium	heart
4	chr19:35740600-35748000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:35740600-35748200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:35740800-35741600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:35740800-35741600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr19:35740800-35741600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:35740800-35741600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:35740800-35741800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr19:35740800-35744200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr19:35740800-35747000	Weak transcription	Small Intestine	intestine
13	chr19:35740800-35747400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr19:35741000-35741600	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:35741000-35741600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:35741000-35741600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:35741000-35741600	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
18	chr19:35741000-35741600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
19	chr19:35741000-35741600	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
20	chr19:35741000-35741600	Transcr. at gene 5' and 3'	Gastric	stomach
21	chr19:35741000-35741600	Enhancers	Spleen	Spleen
22	chr19:35741000-35744400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:35741000-35746000	Weak transcription	Fetal Heart	heart
24	chr19:35741000-35747400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr19:35741000-35748000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:35741000-35748200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:35741200-35741600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:35741200-35741600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
29	chr19:35741200-35741600	Transcr. at gene 5' and 3'	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:35741200-35741600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr19:35741200-35741600	Transcr. at gene 5' and 3'	Pancreas	Pancrea
32	chr19:35741200-35741600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
33	chr19:35741200-35741600	Enhancers	GM12878-XiMat	blood
34	chr19:35741200-35741600	Active TSS	Hela-S3	cervix
35	chr19:35741200-35741600	Flanking Active TSS	HepG2	liver
36	chr19:35741200-35741800	Enhancers	Stomach Mucosa	stomach
37	chr19:35741200-35742000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr19:35741200-35742000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:35741200-35742400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:35741200-35742600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:35741200-35744600	Weak transcription	Right Ventricle	heart
42	chr19:35741200-35744800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr19:35741200-35745400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:35741200-35758000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr19:35741400-35741600	Genic enhancers	H1 Cell Line	embryonic stem cell
46	chr19:35741400-35741600	Bivalent/Poised TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:35741400-35741600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:35741400-35741600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
49	chr19:35741400-35741600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:35741400-35741600	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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