Variant report

Variant	rs2066629
Chromosome Location	chr13:50761018-50761019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50760379..50762064-chr13:50762698..50765040,2	MCF-7	breast:
2	chr13:50760644..50762180-chr13:51484579..51486384,2	K562	blood:
3	chr13:50760751..50763026-chr13:50764373..50766743,2	K562	blood:
4	chr13:50760570..50765179-chr13:50765243..50769828,5	K562	blood:
5	chr13:50760566..50762913-chr13:51108077..51110898,2	MCF-7	breast:
6	chr13:50749766..50752648-chr13:50760518..50762559,2	MCF-7	breast:
7	chr13:50696202..50700492-chr13:50759152..50762847,4	K562	blood:

Variant related genes	Relation type
ENSG00000233672	Chromatin interaction
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 74 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1007852	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs1965800	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs2049286	1.00[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2066632	0.89[JPT][hapmap];0.81[YRI][hapmap]
rs2066634	0.83[JPT][hapmap]
rs2066639	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2066640	1.00[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2066654	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2580187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2703079	0.83[JPT][hapmap]
rs2703082	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2740516	0.89[JPT][hapmap];0.88[YRI][hapmap]
rs2740521	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2740522	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2740523	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2765763	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1041501	chr13:50683189-50795195	Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv900076	chr13:50710579-50912578	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:74)

SNP	Gene	Cis/trans	Tissue	Source
rs2066629	HSPA6	trans	multi-tissue	Pritchard
rs2066629	HSS00332757	trans	multi-tissue	Pritchard
rs2066629	hCT2254710	trans	multi-tissue	Pritchard
rs2066629	PAGE2	cis	Liver	GTEx
rs2066629	VKORC1L1	trans	multi-tissue	Pritchard
rs2066629	IGHJ4	cis	Liver	GTEx
rs2066629	C3orf38	trans	multi-tissue	Pritchard
rs2066629	ATP7B	cis	cerebellum	SCAN
rs2066629	CTNNA1	cis	Liver	GTEx
rs2066629	ANKLE2	cis	Liver	GTEx
rs2066629	NM_019049	trans	multi-tissue	Pritchard
rs2066629	LOC729856	cis	Liver	GTEx
rs2066629	hCT1970673	trans	multi-tissue	Pritchard
rs2066629	HSPA6	cis	Liver	GTEx
rs2066629	AL833452	trans	multi-tissue	Pritchard
rs2066629	SLC35D3	cis	Liver	GTEx
rs2066629	GPR119	trans	multi-tissue	Pritchard
rs2066629	HSS00051980	trans	multi-tissue	Pritchard
rs2066629	hCT9855.3	trans	multi-tissue	Pritchard
rs2066629	ASAM	cis	Liver	GTEx
rs2066629	CXYorf2	trans	multi-tissue	Pritchard
rs2066629	PAGE2	trans	multi-tissue	Pritchard
rs2066629	GPR119	cis	Liver	GTEx
rs2066629	NCRNA00105	cis	Liver	GTEx
rs2066629	SNORA70	trans	multi-tissue	Pritchard
rs2066629	NTSR1	trans	multi-tissue	Pritchard
rs2066629	SPATA12	trans	multi-tissue	Pritchard
rs2066629	PMS2L2	trans	multi-tissue	Pritchard
rs2066629	C9orf82	trans	multi-tissue	Pritchard
rs2066629	HES7	trans	multi-tissue	Pritchard
rs2066629	ARF1	cis	Liver	GTEx
rs2066629	SRRM2	cis	Liver	GTEx
rs2066629	AK021617	trans	multi-tissue	Pritchard
rs2066629	POU5F1P4	cis	Liver	GTEx
rs2066629	RP11-506K6.3	trans	multi-tissue	Pritchard
rs2066629	OSBP2	trans	multi-tissue	Pritchard
rs2066629	SOBP	cis	Liver	GTEx
rs2066629	Contig46187_RC	trans	multi-tissue	Pritchard
rs2066629	VKORC1L1	cis	Liver	GTEx
rs2066629	C3orf38	cis	Liver	GTEx
rs2066629	MTA1	cis	Liver	GTEx
rs2066629	XM_120661	trans	multi-tissue	Pritchard
rs2066629	MTA1	trans	multi-tissue	Pritchard
rs2066629	KIAA1486	cis	Liver	GTEx
rs2066629	DENND1B	cis	Liver	GTEx
rs2066629	hCT1959389	trans	multi-tissue	Pritchard
rs2066629	SPATA12	cis	Liver	GTEx
rs2066629	HNRPU	trans	multi-tissue	Pritchard
rs2066629	HNRNPU	cis	Liver	GTEx
rs2066629	NTSR2	cis	Liver	GTEx
rs2066629	hCT1786921.2	trans	multi-tissue	Pritchard
rs2066629	IGHV4-31	trans	multi-tissue	Pritchard
rs2066629	C9orf82	cis	Liver	GTEx
rs2066629	SNORA70	cis	Liver	GTEx
rs2066629	AF268613	trans	multi-tissue	Pritchard
rs2066629	NTSR1	cis	Liver	GTEx
rs2066629	Contig40516_RC	trans	multi-tissue	Pritchard
rs2066629	Contig37397_RC	trans	multi-tissue	Pritchard
rs2066629	hCT2324815	trans	multi-tissue	Pritchard
rs2066629	OSBP2	cis	Liver	GTEx
rs2066629	TMEM106B	trans	multi-tissue	Pritchard
rs2066629	TYW1	cis	Liver	GTEx
rs2066629	BICD2	cis	Liver	GTEx
rs2066629	ADAMTS14	cis	Liver	GTEx
rs2066629	BICD2	trans	multi-tissue	Pritchard
rs2066629	CTNNA1	trans	multi-tissue	Pritchard
rs2066629	HES7	cis	Liver	GTEx
rs2066629	SLC35D3	trans	multi-tissue	Pritchard
rs2066629	NTSR2	trans	multi-tissue	Pritchard
rs2066629	NM_024769	trans	multi-tissue	Pritchard
rs2066629	TMEM106B	cis	Liver	GTEx
rs2066629	SRRM2	trans	multi-tissue	Pritchard
rs2066629	PHF11	cis	multi-tissue	Pritchard
rs2066629	AK023803	trans	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50760000-50761200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr13:50760000-50761200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr13:50760200-50761200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr13:50760200-50761600	Active TSS	K562	blood
5	chr13:50760400-50761200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr13:50760400-50761200	Bivalent/Poised TSS	HepG2	liver
7	chr13:50760400-50764000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr13:50760600-50761200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr13:50760600-50761400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr13:50760600-50789200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:50760800-50761200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr13:50760800-50762200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr13:50760800-50762400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:50761000-50761400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr13:50761000-50762400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr13:50761000-50766400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr13:50761000-50766600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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