Variant report

Variant	rs2377470
Chromosome Location	chr1:226317079-226317080
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226247784..226253760-chr1:226305545..226317702,29	MCF-7	breast:
2	chr1:226316368..226319027-chr1:226319079..226321600,2	K562	blood:
3	chr1:226313181..226318051-chr1:226333070..226339347,8	MCF-7	breast:
4	chr1:226313378..226317234-chr1:226370614..226375969,8	MCF-7	breast:
5	chr1:226315712..226317233-chr1:226376032..226378818,2	MCF-7	breast:
6	chr1:226315099..226318031-chr1:226330803..226332605,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182827	Chromatin interaction
ENSG00000272562	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000234478	Chromatin interaction
ENSG00000223570	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12060155	0.81[ASN][1000 genomes]
rs12066979	0.81[ASN][1000 genomes]
rs12096737	0.81[ASN][1000 genomes]
rs28737326	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4012723	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61835246	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61835247	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426106	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6692849	0.81[ASN][1000 genomes]
rs7522361	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription 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 miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	esv1792510	chr1:226277560-226323824	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription 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	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2377470	H3F3A	cis	Esophagus Mucosa	GTEx
rs2377470	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226310400-226333800	Weak transcription	Small Intestine	intestine
2	chr1:226310600-226319800	Weak transcription	Right Ventricle	heart
3	chr1:226310600-226322400	Weak transcription	Right Atrium	heart
4	chr1:226310800-226331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:226312800-226321000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:226313000-226323200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:226313400-226322000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:226313400-226322600	Weak transcription	Brain Angular Gyrus	brain
9	chr1:226315000-226317200	Enhancers	Placenta	Placenta
10	chr1:226315000-226317200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:226315200-226317200	Enhancers	HSMMtube	muscle
12	chr1:226315400-226318800	Weak transcription	K562	blood
13	chr1:226315600-226322600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:226315800-226317800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:226315800-226320600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:226316000-226320200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:226316000-226320600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:226316000-226322000	Enhancers	Primary B cells from cord blood	blood
19	chr1:226316000-226324000	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:226316200-226320000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:226316400-226317200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:226316400-226317200	Enhancers	Gastric	stomach
23	chr1:226316600-226317200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:226316600-226317200	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr1:226316600-226320000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:226316600-226320000	Weak transcription	Colonic Mucosa	Colon
27	chr1:226316600-226320400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:226316600-226322600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:226316800-226318400	Weak transcription	NH-A	brain
30	chr1:226316800-226319400	Weak transcription	Esophagus	oesophagus
31	chr1:226316800-226320400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:226316800-226320400	Weak transcription	Pancreas	Pancrea
33	chr1:226316800-226320400	Weak transcription	HMEC	breast
34	chr1:226316800-226320400	Weak transcription	NHEK	skin
35	chr1:226316800-226320600	Weak transcription	Fetal Intestine Large	intestine
36	chr1:226316800-226323000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:226317000-226317200	Enhancers	Stomach Mucosa	stomach
38	chr1:226317000-226317800	Enhancers	HepG2	liver
39	chr1:226317000-226319000	Weak transcription	Fetal Lung	lung
40	chr1:226317000-226319800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:226317000-226319800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:226317000-226320000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:226317000-226320000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:226317000-226320000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:226317000-226320400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:226317000-226320400	Weak transcription	HSMM	muscle
47	chr1:226317000-226320600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:226317000-226322200	Weak transcription	Fetal Heart	heart

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