Variant report

Variant	rs677488
Chromosome Location	chr11:66324762-66324763
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66320797..66323676-chr11:66324409..66326374,2	MCF-7	breast:
2	chr11:66323180..66325641-chr11:66328411..66330736,2	MCF-7	breast:
3	chr11:66311873..66314750-chr11:66320969..66327300,6	K562	blood:

Variant related genes	Relation type
ENSG00000174165	Chromatin interaction
ENSG00000248746	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:40)

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]
rs12577111	0.83[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs12805133	0.83[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs1671062	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs1671063	0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs1671064	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];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	0.83[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs1791686	0.87[ASN][1000 genomes]
rs1815739	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2000939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276138	0.83[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap]
rs2279863	0.90[JPT][hapmap]
rs3018318	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741363	0.83[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap]
rs486584	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs4930387	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs498045	0.88[GIH][hapmap]
rs503250	0.83[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs508443	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs509556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];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]
rs535211	0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs540874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];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	0.83[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs560556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs577023	0.88[GIH][hapmap];0.95[JPT][hapmap]
rs580910	0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs615205	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618838	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];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]
rs678397	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692892	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7925108	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs8432	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs677488	CCS	cis	lymphoblastoid	seeQTL
rs677488	CCS	cis	multi-tissue	Pritchard
rs677488	KDM2A	cis	cerebellum	SCAN
rs677488	PRDX5	cis	cerebellum	SCAN
rs677488	ACTN3	cis	lymphoblastoid	seeQTL
rs677488	ACTN3	cis	Muscle Skeletal	GTEx
rs677488	CTSF	cis	parietal	SCAN
rs677488	CTSF	cis	cerebellum	SCAN
rs677488	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs677488	YIF1A	cis	cerebellum	SCAN
rs677488	UNC93B1	cis	cerebellum	SCAN
rs677488	CCDC85B	cis	parietal	SCAN
rs677488	GANAB	cis	parietal	SCAN
rs677488	YIF1A	cis	parietal	SCAN
rs677488	SYT12	cis	parietal	SCAN
rs677488	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs677488	CDC42EP2	cis	cerebellum	SCAN

Chromatin state (count:26 , 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	chr11:66316400-66325200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:66316800-66325800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:66317000-66324800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:66319000-66337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:66321400-66330400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:66321400-66331600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:66321800-66326400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr11:66321800-66326400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:66321800-66326400	Weak transcription	Gastric	stomach
12	chr11:66322200-66325800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:66322600-66331400	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr11:66323000-66325400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:66323600-66326400	Weak transcription	Pancreas	Pancrea
16	chr11:66323800-66324800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr11:66323800-66325000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:66323800-66325000	Weak transcription	Fetal Muscle Leg	muscle
19	chr11:66324400-66325200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr11:66324600-66324800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:66324600-66324800	Enhancers	Esophagus	oesophagus
22	chr11:66324600-66325000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:66324600-66325000	Bivalent Enhancer	Fetal Brain Female	brain
24	chr11:66324600-66325400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:66324600-66325600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
26	chr11:66324600-66325800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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