Variant report

Variant	rs1894442
Chromosome Location	chr4:3386315-3386316
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	JUND	chr4:3386189-3386364	K562	blood:	n/a	n/a
2	FOS	chr4:3386043-3386414	MCF10A-Er-Src	breast:	n/a	chr4:3386379-3386388
3	MAFF	chr4:3386174-3386396	HepG2	liver:	n/a	n/a
4	MAFF	chr4:3386161-3386385	K562	blood:	n/a	n/a
5	CEBPB	chr4:3386160-3386371	Hela-S3	cervix:	n/a	chr4:3386198-3386209
6	FOS	chr4:3386065-3386434	MCF10A-Er-Src	breast:	n/a	chr4:3386379-3386388
7	MYC	chr4:3386220-3386398	K562	blood:	n/a	n/a
8	NFYB	chr4:3386272-3386497	K562	blood:	n/a	chr4:3386374-3386386 chr4:3386375-3386389 chr4:3386375-3386390 chr4:3386375-3386390 chr4:3386377-3386387
9	CEBPB	chr4:3386120-3386463	MCF-7	breast:	n/a	chr4:3386198-3386209
10	POLR2A	chr4:3386251-3386768	HUVEC	blood vessel:	n/a	n/a
11	STAT3	chr4:3386062-3386396	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr4:3386052-3386376	A549	lung:	n/a	chr4:3386198-3386209
13	STAT3	chr4:3386064-3386353	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr4:3386059-3386500	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr4:3386029-3386395	HepG2	liver:	n/a	chr4:3386198-3386209
16	CTCF	chr4:3386260-3386410	SAEC	small airway:	n/a	n/a
17	ATF1	chr4:3386197-3386397	K562	blood:	n/a	n/a
18	MAFK	chr4:3386160-3386403	HepG2	liver:	n/a	n/a
19	STAT3	chr4:3386036-3386375	MCF10A-Er-Src	breast:	n/a	n/a
20	MAFK	chr4:3386174-3386448	K562	blood:	n/a	n/a
21	MYC	chr4:3386056-3386416	MCF10A-Er-Src	breast:	n/a	n/a
22	FOS	chr4:3386025-3386424	MCF10A-Er-Src	breast:	n/a	chr4:3386379-3386388
23	CEBPB	chr4:3386035-3386386	IMR90	lung:	n/a	chr4:3386198-3386209
24	MAFK	chr4:3386108-3386437	HepG2	liver:	n/a	n/a
25	CEBPB	chr4:3386080-3386364	K562	blood:	n/a	chr4:3386198-3386209
26	MAFK	chr4:3386159-3386403	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3384020..3386555-chr4:3387570..3389636,2	K562	blood:
2	chr4:3386285..3389665-chr4:3485168..3487566,3	MCF-7	breast:

Variant related genes	Relation type
RGS12	TF binding region
ENSG00000159788	Chromatin interaction
ENSG00000175920	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10029047	0.80[EUR][1000 genomes]
rs12644442	0.83[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13109976	0.81[JPT][hapmap]
rs13116176	0.81[JPT][hapmap]
rs13127597	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13152128	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1320762	0.85[JPT][hapmap]
rs1320763	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1406674	0.80[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs1406675	0.80[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs16843157	0.80[JPT][hapmap]
rs16844301	0.82[JPT][hapmap]
rs16844307	0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs16844309	0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs17797467	0.83[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1962767	0.80[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs3213506	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs3213507	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3752442	0.81[JPT][hapmap]
rs4690090	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4690098	0.81[JPT][hapmap]
rs6446740	0.80[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.80[EUR][1000 genomes]
rs6828057	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9790656	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs9995777	0.89[EUR][1000 genomes]

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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1894442	DOK7	cis	cerebellum	SCAN
rs1894442	SLBP	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3372200-3386400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:3373000-3389000	Weak transcription	Psoas Muscle	Psoas
3	chr4:3373400-3388400	Weak transcription	Fetal Kidney	kidney
4	chr4:3373400-3388800	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:3375000-3389200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:3375200-3387000	Weak transcription	Right Atrium	heart
7	chr4:3375400-3386400	Weak transcription	Brain Substantia Nigra	brain
8	chr4:3375400-3386600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:3375400-3389600	Weak transcription	NHLF	lung
10	chr4:3375600-3387000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr4:3378200-3388800	Weak transcription	Fetal Heart	heart
12	chr4:3378400-3386400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:3378400-3388800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:3378400-3389000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:3378400-3389200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:3378400-3389200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:3378400-3390400	Weak transcription	Ovary	ovary
18	chr4:3378600-3386400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:3378600-3389600	Weak transcription	Aorta	Aorta
20	chr4:3378800-3386400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:3380800-3386800	Weak transcription	Primary T cells from cord blood	blood
22	chr4:3381000-3389000	Weak transcription	Fetal Brain Male	brain
23	chr4:3381000-3389200	Weak transcription	HSMMtube	muscle
24	chr4:3382200-3386400	Weak transcription	Adipose Nuclei	Adipose
25	chr4:3382200-3386400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:3382200-3386800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr4:3382400-3386400	Weak transcription	Fetal Intestine Large	intestine
28	chr4:3382400-3386400	Weak transcription	Fetal Lung	lung
29	chr4:3382400-3386400	Weak transcription	Gastric	stomach
30	chr4:3382600-3386400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:3382600-3386400	Weak transcription	Esophagus	oesophagus
32	chr4:3382600-3386400	Weak transcription	Fetal Muscle Leg	muscle
33	chr4:3382600-3389000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:3382600-3389000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:3383000-3386400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:3383200-3389600	Weak transcription	Fetal Brain Female	brain
37	chr4:3383400-3386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:3383600-3386400	Weak transcription	Spleen	Spleen
39	chr4:3383600-3386600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr4:3383600-3386600	Weak transcription	Brain Germinal Matrix	brain
41	chr4:3383600-3386800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:3383600-3388000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:3383800-3386800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr4:3384200-3386600	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr4:3384400-3386400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:3384600-3387600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:3385600-3386600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:3386000-3386400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:3386000-3386400	Enhancers	Fetal Intestine Small	intestine
50	chr4:3386000-3386800	Genic enhancers	Fetal Stomach	stomach

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