Variant report

Variant	rs2303652
Chromosome Location	chr19:42703833-42703834
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:113)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:113 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr19:42703803-42704341	K562	blood:	n/a	n/a
2	CCNT2	chr19:42703622-42704119	K562	blood:	n/a	n/a
3	STAT3	chr19:42703768-42703942	MCF10A-Er-Src	breast:	n/a	n/a
4	RELA	chr19:42703310-42704502	GM18505	blood:	n/a	n/a
5	ELF1	chr19:42703511-42704318	K562	blood:	n/a	n/a
6	ELF1	chr19:42703514-42704485	GM12878	blood:	n/a	n/a
7	TAF1	chr19:42703723-42704236	GM12878	blood:	n/a	n/a
8	RELA	chr19:42703175-42704303	GM19193	blood:	n/a	n/a
9	FOXM1	chr19:42703625-42704399	GM12878	blood:	n/a	n/a
10	STAT5A	chr19:42702996-42704541	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:42703602-42704460	K562	blood:	n/a	n/a
12	POLR2A	chr19:42703459-42704461	K562	blood:	n/a	n/a
13	HMGN3	chr19:42703587-42704099	K562	blood:	n/a	n/a
14	TCF12	chr19:42703642-42704042	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:42703656-42704505	K562	blood:	n/a	n/a
16	MAZ	chr19:42703139-42704339	GM12878	blood:	n/a	chr19:42704005-42704015
17	RELA	chr19:42703204-42704498	GM19099	blood:	n/a	n/a
18	CBX3	chr19:42703292-42704563	K562	blood:	n/a	n/a
19	MYC	chr19:42703718-42704557	K562	blood:	n/a	chr19:42704005-42704015
20	EP300	chr19:42703776-42704264	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:42703097-42704513	GM12878	blood:	n/a	n/a
22	TCF3	chr19:42703664-42704119	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:42702982-42704337	GM12878	blood:	n/a	n/a
24	GABPA	chr19:42703622-42704431	K562	blood:	n/a	n/a
25	RUNX3	chr19:42702844-42704443	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:42703139-42704321	GM19099	blood:	n/a	n/a
27	TBL1XR1	chr19:42703281-42704372	GM12878	blood:	n/a	n/a
28	GATA1	chr19:42703572-42704901	PBDE	blood:	n/a	n/a
29	CTCF	chr19:42703784-42703909	GM12891	blood:	n/a	n/a
30	CTCF	chr19:42703780-42703930	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:42703001-42704348	GM12892	blood:	n/a	n/a
32	POLR2A	chr19:42702925-42704377	GM12878	blood:	n/a	n/a
33	MYC	chr19:42703819-42703943	K562	blood:	n/a	n/a
34	PML	chr19:42703173-42704469	GM12878	blood:	n/a	n/a
35	ELF1	chr19:42703829-42704357	K562	blood:	n/a	n/a
36	ATF2	chr19:42703183-42704404	GM12878	blood:	n/a	n/a
37	SIN3A	chr19:42703812-42704407	GM12878	blood:	n/a	n/a
38	MAX	chr19:42703073-42704507	GM12878	blood:	n/a	chr19:42704005-42704015
39	SP1	chr19:42703669-42704392	GM12878	blood:	n/a	n/a
40	MAX	chr19:42703465-42704414	K562	blood:	n/a	chr19:42704005-42704015
41	POLR2A	chr19:42703114-42704633	GM18505	blood:	n/a	n/a
42	POLR2A	chr19:42702968-42704439	GM12892	blood:	n/a	n/a
43	POLR2A	chr19:42703534-42704300	K562	blood:	n/a	n/a
44	MAX	chr19:42703619-42704334	K562	blood:	n/a	chr19:42704005-42704015
45	TBL1XR1	chr19:42703786-42704410	K562	blood:	n/a	n/a
46	MXI1	chr19:42703714-42704568	GM12878	blood:	n/a	n/a
47	SIN3AK20	chr19:42703572-42704371	K562	blood:	n/a	n/a
48	POLR2A	chr19:42703070-42704374	GM18951	blood:	n/a	n/a
49	BCLAF1	chr19:42703148-42704394	GM12878	blood:	n/a	n/a
50	YY1	chr19:42703712-42704043	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:42702882..42705011-chr19:42731781..42733580,2	MCF-7	breast:
2	chr19:42701476..42703975-chr19:42745160..42748924,4	K562	blood:
3	chr19:42692989..42696202-chr19:42701763..42704726,3	K562	blood:
4	chr19:42672373..42674128-chr19:42703311..42705172,2	K562	blood:
5	chr19:42637643..42639278-chr19:42702596..42704776,2	K562	blood:
6	chr19:42702613..42704182-chr19:42721440..42723346,2	K562	blood:
7	chr19:42701066..42704038-chr19:42771029..42772708,2	K562	blood:

No data

Variant related genes	Relation type
POU2F2	TF binding region
ENSG00000254887	Chromatin interaction
ENSG00000204957	Chromatin interaction
ENSG00000160570	Chromatin interaction
ENSG00000079432	Chromatin interaction
ENSG00000266226	Chromatin interaction
ENSG00000105723	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10407506	0.80[LWK][hapmap];0.83[YRI][hapmap]
rs10410185	0.82[CHB][hapmap]
rs10410198	0.82[CHB][hapmap]
rs10410698	0.82[CHB][hapmap]
rs10500285	0.93[GIH][hapmap];0.91[TSI][hapmap]
rs11878620	0.81[ASW][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11880124	0.81[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11883412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1206009	0.82[CHB][hapmap]
rs1206027	0.82[CHB][hapmap]
rs1206029	0.82[CHB][hapmap]
rs1206033	0.82[CHB][hapmap]
rs1206038	0.82[CHB][hapmap]
rs1206040	0.82[CHB][hapmap]
rs1206041	0.82[CHB][hapmap]
rs1206044	0.82[CHB][hapmap]
rs1613100	0.82[CHB][hapmap]
rs1654623	0.82[CHB][hapmap]
rs1676211	0.82[CHB][hapmap]
rs1676217	0.82[CHB][hapmap]
rs1676221	0.82[CHB][hapmap]
rs1676222	0.82[CHB][hapmap]
rs1685565	0.82[CHB][hapmap]
rs16975663	0.83[ASW][hapmap];0.90[CEU][hapmap];0.83[GIH][hapmap];0.94[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs16975684	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17270169	0.85[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs17342284	0.85[CHB][hapmap]
rs17750207	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2267630	0.82[CHB][hapmap]
rs2302485	0.93[GIH][hapmap];0.91[MEX][hapmap]
rs2537697	0.82[CHB][hapmap]
rs2615614	0.82[CHB][hapmap]
rs28621009	0.82[CHB][hapmap]
rs3745231	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3745233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810148	0.82[CHB][hapmap]
rs3810151	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3826705	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs4141062	0.82[CHB][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap]
rs443239	0.87[TSI][hapmap]
rs454150	0.83[ASW][hapmap];0.81[CEU][hapmap];0.94[LWK][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap]
rs59099214	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62119628	0.86[ASN][1000 genomes]
rs7248379	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251466	0.87[TSI][hapmap]
rs741070	0.82[CHB][hapmap]
rs8108096	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8182491	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs851296	0.82[CHB][hapmap]
rs899661	0.87[TSI][hapmap]
rs9636121	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2303652	DEDD2	cis	multi-tissue	Pritchard
rs2303652	ZNF219	trans	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42696600-42710000	Weak transcription	NH-A	brain
2	chr19:42696600-42712200	Weak transcription	Fetal Kidney	kidney
3	chr19:42697800-42706800	Weak transcription	Ovary	ovary
4	chr19:42697800-42708800	Weak transcription	NHDF-Ad	bronchial
5	chr19:42697800-42710400	Weak transcription	HSMMtube	muscle
6	chr19:42698000-42707600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:42698000-42709800	Weak transcription	HSMM	muscle
8	chr19:42698600-42709800	Weak transcription	HUVEC	blood vessel
9	chr19:42699800-42714000	Weak transcription	Fetal Brain Male	brain
10	chr19:42700200-42708200	Genic enhancers	Spleen	Spleen
11	chr19:42700200-42714600	Strong transcription	Brain Germinal Matrix	brain
12	chr19:42700400-42710400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:42700400-42714600	Strong transcription	Stomach Smooth Muscle	stomach
14	chr19:42700400-42717200	Weak transcription	Psoas Muscle	Psoas
15	chr19:42700400-42719800	Strong transcription	Fetal Stomach	stomach
16	chr19:42700800-42704000	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
17	chr19:42701000-42705000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
18	chr19:42701000-42707200	Genic enhancers	Rectal Mucosa Donor 31	rectum
19	chr19:42701000-42709000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:42701000-42720200	Weak transcription	Fetal Heart	heart
21	chr19:42701200-42704800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr19:42701200-42705800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:42701200-42706400	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr19:42701200-42715200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:42701200-42719800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:42701400-42704000	Strong transcription	Brain Anterior Caudate	brain
27	chr19:42701400-42714400	Strong transcription	Brain Angular Gyrus	brain
28	chr19:42701400-42715200	Strong transcription	Fetal Brain Female	brain
29	chr19:42701600-42708600	Strong transcription	Pancreas	Pancrea
30	chr19:42701600-42708800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:42701600-42710800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:42701600-42715200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr19:42701800-42704200	Strong transcription	Brain Substantia Nigra	brain
34	chr19:42701800-42707200	Strong transcription	Liver	Liver
35	chr19:42702000-42708400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:42702000-42709000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr19:42702000-42710400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:42702000-42710400	Strong transcription	A549	lung
39	chr19:42702000-42711000	Strong transcription	Gastric	stomach
40	chr19:42702000-42714200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:42702000-42715200	Strong transcription	Fetal Intestine Large	intestine
42	chr19:42702000-42719400	Strong transcription	Fetal Intestine Small	intestine
43	chr19:42702200-42704000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:42702200-42706600	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr19:42702200-42708400	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr19:42702200-42711200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr19:42702200-42714400	Strong transcription	Aorta	Aorta
48	chr19:42702400-42704200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr19:42702400-42704200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr19:42702400-42706200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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