Variant report

Variant	rs10753434
Chromosome Location	chr1:227560600-227560601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227551558..227554150-chr1:227559420..227561744,2	MCF-7	breast:
2	chr1:227554260..227555782-chr1:227558774..227561008,2	K562	blood:
3	chr1:227545277..227548710-chr1:227557152..227561579,4	K562	blood:
4	chr1:227556870..227561275-chr1:227563192..227568675,6	K562	blood:
5	chr1:227519023..227520761-chr1:227558780..227560825,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10458380	0.80[ASN][1000 genomes]
rs10799412	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916123	0.80[ASN][1000 genomes]
rs10916124	0.80[ASN][1000 genomes]
rs10916127	0.82[ASN][1000 genomes]
rs10916128	0.83[ASN][1000 genomes]
rs10916129	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12022275	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs12022338	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12023427	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]
rs12028523	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs12047964	0.85[ASN][1000 genomes]
rs12057466	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12062358	0.88[ASN][1000 genomes]
rs12081061	0.81[ASN][1000 genomes]
rs16847682	0.86[ASN][1000 genomes]
rs16847690	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.86[ASN][1000 genomes]
rs3000777	0.82[EUR][1000 genomes]
rs3014272	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3014274	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4075196	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4075861	0.86[ASN][1000 genomes]
rs4233226	0.87[JPT][hapmap]
rs4233227	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4294380	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4489522	0.82[EUR][1000 genomes]
rs4491034	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4531260	0.88[ASN][1000 genomes]
rs4653497	0.86[ASN][1000 genomes]
rs4653498	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4653826	0.87[JPT][hapmap]
rs4653828	0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs4653831	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59718661	0.81[ASN][1000 genomes]
rs61833060	0.86[ASN][1000 genomes]
rs6690898	0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs67343057	0.81[ASN][1000 genomes]
rs7519870	0.85[ASN][1000 genomes]
rs7541775	0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7553358	0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs7555764	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556096	0.80[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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10753434	IMAGE3451454	cis	multi-tissue	Pritchard

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227545800-227571200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:227556800-227560800	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr1:227556800-227560800	Enhancers	Stomach Mucosa	stomach
4	chr1:227556800-227561200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr1:227556800-227561200	Enhancers	HUVEC	blood vessel
6	chr1:227557200-227565400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:227558000-227560600	Enhancers	A549	lung
8	chr1:227558600-227565400	Weak transcription	HSMMtube	muscle
9	chr1:227558600-227565600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:227559000-227565800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:227559800-227560600	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:227560000-227561000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr1:227560000-227561200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:227560000-227561200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:227560000-227565200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:227560000-227565400	Weak transcription	K562	blood
17	chr1:227560200-227560800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:227560400-227560800	Enhancers	Brain Hippocampus Middle	brain
19	chr1:227560600-227561000	Enhancers	Brain Substantia Nigra	brain
20	chr1:227560600-227561000	Flanking Active TSS	A549	lung
21	chr1:227560600-227565400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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