Variant report

Variant	rs61835247
Chromosome Location	chr1:226323974-226323975
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226323029..226325109-chr1:226350142..226352529,2	K562	blood:
2	chr1:226309387..226312243-chr1:226322101..226324468,2	K562	blood:
3	chr1:226322866..226324714-chr1:226373638..226375451,2	MCF-7	breast:
4	chr1:226309744..226312243-chr1:226321771..226324398,3	K562	blood:
5	chr1:226318378..226321338-chr1:226323384..226325455,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182827	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12060155	0.80[ASN][1000 genomes]
rs12066979	0.80[ASN][1000 genomes]
rs12096737	0.80[ASN][1000 genomes]
rs2377470	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28737326	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4012723	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61835246	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426106	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6692849	0.80[ASN][1000 genomes]
rs7522361	0.91[EUR][1000 genomes];0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs61835247	H3F3A	cis	Esophagus Mucosa	GTEx
rs61835247	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226310400-226333800	Weak transcription	Small Intestine	intestine
2	chr1:226310800-226331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:226316000-226324000	Enhancers	Primary B cells from peripheral blood	blood
4	chr1:226317200-226331200	Weak transcription	Placenta	Placenta
5	chr1:226318600-226331600	Weak transcription	NH-A	brain
6	chr1:226319400-226324200	Enhancers	Gastric	stomach
7	chr1:226319600-226331200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:226320000-226324000	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr1:226320000-226324400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:226320800-226334000	Weak transcription	K562	blood
11	chr1:226321000-226331000	Weak transcription	HSMM	muscle
12	chr1:226321200-226331800	Weak transcription	HSMMtube	muscle
13	chr1:226321400-226331600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:226321400-226331600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:226321400-226331800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:226321400-226333800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:226321400-226333800	Weak transcription	GM12878-XiMat	blood
18	chr1:226321800-226331800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:226322000-226324000	Enhancers	Stomach Mucosa	stomach
20	chr1:226322000-226324000	Enhancers	HepG2	liver
21	chr1:226322000-226331600	Weak transcription	Primary B cells from cord blood	blood
22	chr1:226322000-226334400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:226322200-226331600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:226322200-226331800	Weak transcription	HMEC	breast
25	chr1:226322400-226324000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr1:226322600-226324000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr1:226322600-226324000	Bivalent Enhancer	Fetal Muscle Leg	muscle
28	chr1:226322600-226324200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:226322600-226324200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:226322600-226324200	Enhancers	Colonic Mucosa	Colon
31	chr1:226322600-226324400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:226322800-226324000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr1:226322800-226333000	Weak transcription	Brain Substantia Nigra	brain
34	chr1:226323000-226324000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:226323000-226324000	Bivalent Enhancer	Fetal Stomach	stomach
36	chr1:226323000-226324200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:226323200-226324000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:226323200-226324000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr1:226323200-226324000	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr1:226323200-226324000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:226323200-226324000	Enhancers	Fetal Muscle Trunk	muscle
42	chr1:226323200-226324000	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr1:226323200-226324200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:226323200-226324400	Enhancers	Pancreas	Pancrea
45	chr1:226323200-226330600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:226323200-226331200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:226323200-226331800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:226323200-226331800	Weak transcription	Spleen	Spleen
49	chr1:226323200-226333200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:226323200-226333600	Weak transcription	Brain Hippocampus Middle	brain

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