Variant report

Variant	rs9661265
Chromosome Location	chr1:226343049-226343050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226342475..226345121-chr1:226347996..226349840,2	K562	blood:
2	chr1:226338792..226340771-chr1:226341760..226343637,2	K562	blood:
3	chr1:226333102..226335693-chr1:226342114..226343895,2	K562	blood:

Variant related genes	Relation type
ENSG00000182827	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10495244	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10915951	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915955	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12033959	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12076062	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12087091	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16860230	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3008193	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61836880	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9729045	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9988629	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9661265	H3F3A	cis	Nerve Tibial	GTEx
rs9661265	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs9661265	ACBD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226323200-226344600	Weak transcription	Brain Angular Gyrus	brain
2	chr1:226323600-226346000	Weak transcription	Fetal Heart	heart
3	chr1:226323800-226355000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:226324000-226372800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:226324400-226346200	Weak transcription	Pancreas	Pancrea
6	chr1:226329600-226353800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:226330600-226354200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:226330800-226354200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:226331000-226353800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:226331000-226353800	Strong transcription	Adipose Nuclei	Adipose
11	chr1:226331000-226354000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:226331000-226355200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:226331600-226346200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:226331600-226353600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:226331600-226353800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr1:226331600-226354200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:226331600-226355600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:226331800-226353800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:226331800-226353800	Strong transcription	Liver	Liver
20	chr1:226332200-226346600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:226333000-226356400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:226333600-226343200	Strong transcription	Fetal Intestine Large	intestine
23	chr1:226333800-226343200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:226333800-226354400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:226336800-226343400	Strong transcription	GM12878-XiMat	blood
26	chr1:226337800-226352600	Strong transcription	A549	lung
27	chr1:226338000-226350800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:226338200-226354000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:226338400-226344600	Strong transcription	HSMM	muscle
30	chr1:226338400-226344800	Strong transcription	NHDF-Ad	bronchial
31	chr1:226338400-226348400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:226338400-226351000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:226338400-226353800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:226338400-226353800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:226338400-226354200	Strong transcription	Placenta	Placenta
36	chr1:226338400-226354400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:226338600-226353600	Strong transcription	Stomach Smooth Muscle	stomach
38	chr1:226339000-226344600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:226340200-226346400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:226340200-226353200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:226340400-226343600	Weak transcription	Hela-S3	cervix
42	chr1:226340400-226344000	Weak transcription	HMEC	breast
43	chr1:226340400-226346200	Weak transcription	Fetal Brain Male	brain
44	chr1:226340400-226349200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:226340400-226369600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:226341000-226343800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:226341400-226346000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:226341400-226346800	Weak transcription	Small Intestine	intestine
49	chr1:226341600-226348600	Weak transcription	Stomach Mucosa	stomach
50	chr1:226341600-226348800	Genic enhancers	Primary B cells from peripheral blood	blood

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