Variant report

Variant	rs12644442
Chromosome Location	chr4:3387571-3387572
allele	A/G
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	MYC	chr4:3387112-3388675	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:3386875-3388105	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr4:3387364-3387696	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:3387044-3387706	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr4:3386902-3387593	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3294234..3297919-chr4:3387466..3390148,3	MCF-7	breast:
2	chr4:3386285..3389665-chr4:3485168..3487566,3	MCF-7	breast:

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

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10029047	0.87[EUR][1000 genomes]
rs13116176	0.80[JPT][hapmap]
rs13127597	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13152128	0.96[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1320763	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1406674	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1406675	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs16844307	0.90[JPT][hapmap]
rs16844309	0.86[JPT][hapmap]
rs17797467	0.96[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1894442	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]
rs1962767	0.96[CEU][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs3213506	0.90[JPT][hapmap]
rs4690090	0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs6446740	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs6828057	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9790656	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9995777	0.92[CEU][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv428435	chr4:3386773-3623321	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3373000-3389000	Weak transcription	Psoas Muscle	Psoas
2	chr4:3373400-3388400	Weak transcription	Fetal Kidney	kidney
3	chr4:3373400-3388800	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:3375000-3389200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:3375400-3389600	Weak transcription	NHLF	lung
6	chr4:3378200-3388800	Weak transcription	Fetal Heart	heart
7	chr4:3378400-3388800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:3378400-3389000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:3378400-3389200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:3378400-3389200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:3378400-3390400	Weak transcription	Ovary	ovary
12	chr4:3378600-3389600	Weak transcription	Aorta	Aorta
13	chr4:3381000-3389000	Weak transcription	Fetal Brain Male	brain
14	chr4:3381000-3389200	Weak transcription	HSMMtube	muscle
15	chr4:3382600-3389000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:3382600-3389000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:3383200-3389600	Weak transcription	Fetal Brain Female	brain
18	chr4:3383600-3388000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:3384600-3387600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:3386200-3387800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:3386200-3387800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:3386200-3387800	Enhancers	Right Ventricle	heart
23	chr4:3386200-3388000	Flanking Active TSS	HMEC	breast
24	chr4:3386200-3388000	Flanking Active TSS	NHEK	skin
25	chr4:3386200-3388200	Enhancers	Lung	lung
26	chr4:3386200-3388200	Flanking Active TSS	HepG2	liver
27	chr4:3386200-3390000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:3386200-3391400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:3386400-3387600	Active TSS	Brain Hippocampus Middle	brain
30	chr4:3386400-3387600	Enhancers	Fetal Muscle Leg	muscle
31	chr4:3386400-3387800	Flanking Active TSS	Esophagus	oesophagus
32	chr4:3386400-3388000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:3386400-3388000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr4:3386400-3388000	Enhancers	NH-A	brain
35	chr4:3386400-3388200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr4:3386400-3388200	Enhancers	Fetal Muscle Trunk	muscle
37	chr4:3386400-3388200	Enhancers	Spleen	Spleen
38	chr4:3386400-3390800	Enhancers	Fetal Lung	lung
39	chr4:3386400-3391200	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr4:3386600-3387600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr4:3386600-3387600	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr4:3386600-3387800	Enhancers	Primary B cells from cord blood	blood
43	chr4:3386600-3387800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
44	chr4:3386600-3387800	Enhancers	Primary hematopoietic stem cells	blood
45	chr4:3386600-3387800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr4:3386600-3387800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:3386600-3390800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:3386600-3392400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:3386600-3393800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:3386800-3387600	Enhancers	Primary neutrophils fromperipheralblood	blood

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