Variant report

Variant	rs2000939
Chromosome Location	chr11:66325830-66325831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66324925..66326614-chr11:66329885..66331523,2	MCF-7	breast:
2	chr11:66320797..66323676-chr11:66324409..66326374,2	MCF-7	breast:
3	chr11:66325723..66328064-chr11:66383615..66385386,2	K562	blood:
4	chr11:66311873..66314750-chr11:66320969..66327300,6	K562	blood:
5	chr11:66325010..66327957-chr11:66384615..66387418,2	K562	blood:
6	chr11:66311617..66317579-chr11:66325496..66333927,8	MCF-7	breast:
7	chr11:66317473..66319701-chr11:66325756..66327731,2	K562	blood:

Variant related genes	Relation type
ENSG00000174165	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000248746	Chromatin interaction
ENSG00000248643	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10736656	0.86[ASN][1000 genomes]
rs10791882	0.94[ASN][1000 genomes]
rs1127894	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1671062	0.86[ASN][1000 genomes]
rs1671063	0.83[ASN][1000 genomes]
rs1671064	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1671065	0.86[ASN][1000 genomes]
rs1700189	0.83[ASN][1000 genomes]
rs1791684	0.82[ASN][1000 genomes]
rs1791686	0.87[ASN][1000 genomes]
rs1815739	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3018318	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs486584	0.92[ASN][1000 genomes]
rs503250	0.80[ASN][1000 genomes]
rs509556	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531490	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs540874	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs545009	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs556759	0.80[ASN][1000 genomes]
rs560556	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572846	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs615205	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618838	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs630021	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs677488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678397	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8432	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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	91 gene(s)	inside rSNPs	diseases
3	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv897787	chr11:66300348-66347850	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv897788	chr11:66319262-66347850	Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2000939	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs2000939	ACTN3	cis	Muscle Skeletal	GTEx
rs2000939	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs2000939	CCS	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66314400-66327000	Weak transcription	Right Atrium	heart
2	chr11:66314800-66326600	Weak transcription	Psoas Muscle	Psoas
3	chr11:66319000-66337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:66321400-66330400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:66321400-66331600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:66321800-66326400	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:66321800-66326400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:66321800-66326400	Weak transcription	Gastric	stomach
9	chr11:66322600-66331400	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr11:66323600-66326400	Weak transcription	Pancreas	Pancrea
11	chr11:66324800-66326400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr11:66324800-66326400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr11:66325000-66326400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:66325000-66326600	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr11:66325000-66329200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:66325200-66326000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:66325400-66327800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:66325800-66326400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr11:66325800-66326800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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