Variant report

Variant	rs4297841
Chromosome Location	chr2:20386660-20386661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20100444..20102626-chr2:20384873..20387447,2	K562	blood:
2	chr2:20377278..20381105-chr2:20382551..20387503,5	K562	blood:
3	chr2:20306400..20314350-chr2:20385971..20392665,10	MCF-7	breast:
4	chr2:20384920..20386704-chr2:20549838..20552413,2	MCF-7	breast:
5	chr2:20337465..20342202-chr2:20382545..20388364,6	MCF-7	breast:
6	chr2:20383626..20385611-chr2:20385923..20390219,5	MCF-7	breast:
7	chr2:20386118..20389028-chr2:20389700..20391555,2	K562	blood:

Variant related genes	Relation type
ENSG00000271991	Chromatin interaction
ENSG00000234378	Chromatin interaction
ENSG00000055917	Chromatin interaction
ENSG00000183891	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11096642	0.87[CEU][hapmap]
rs11096643	0.89[ASN][1000 genomes]
rs11673796	0.87[CEU][hapmap];0.86[AMR][1000 genomes]
rs11694854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12474399	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12475147	0.88[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs35755926	0.88[AMR][1000 genomes]
rs3924843	0.88[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs4358082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531217	0.89[AMR][1000 genomes];0.82[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	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1005524	chr2:20349343-20388138	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1001531	chr2:20350751-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1007926	chr2:20350751-20393557	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20377200-20388200	Enhancers	Stomach Mucosa	stomach
2	chr2:20377400-20390000	Enhancers	Placenta	Placenta
3	chr2:20381400-20387200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:20381600-20387400	Enhancers	NH-A	brain
5	chr2:20381600-20388000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:20382200-20386800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:20383600-20386800	Enhancers	HSMM	muscle
8	chr2:20383800-20389400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:20384200-20386800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr2:20384200-20388800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:20384200-20389400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr2:20384200-20389600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr2:20384400-20387000	Enhancers	Primary hematopoietic stem cells	blood
14	chr2:20384400-20387000	Enhancers	Fetal Muscle Leg	muscle
15	chr2:20384400-20389800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:20384600-20389400	Enhancers	A549	lung
17	chr2:20384600-20391800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:20384600-20392000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:20384600-20400000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:20384800-20388000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:20384800-20389200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr2:20384800-20389600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr2:20385000-20387600	Flanking Active TSS	HepG2	liver
24	chr2:20385200-20391800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:20385400-20386800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:20385400-20388800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:20385600-20386800	Genic enhancers	Fetal Intestine Small	intestine
28	chr2:20385800-20386800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr2:20385800-20387400	Enhancers	GM12878-XiMat	blood
30	chr2:20385800-20388000	Weak transcription	Fetal Lung	lung
31	chr2:20385800-20391000	Weak transcription	Gastric	stomach
32	chr2:20386000-20387000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:20386000-20387000	Weak transcription	Fetal Stomach	stomach
34	chr2:20386000-20389200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr2:20386000-20391200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:20386200-20387000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:20386200-20387200	Weak transcription	Esophagus	oesophagus
38	chr2:20386200-20387800	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr2:20386200-20389400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:20386200-20396000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:20386200-20401400	Weak transcription	Spleen	Spleen
42	chr2:20386400-20386800	Weak transcription	Lung	lung
43	chr2:20386400-20387200	Enhancers	K562	blood
44	chr2:20386400-20387400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:20386400-20387400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:20386400-20387400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr2:20386400-20387400	Enhancers	Fetal Intestine Large	intestine
48	chr2:20386400-20388000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:20386400-20389600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:20386400-20389600	Weak transcription	NHEK	skin

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