Variant report

Variant	rs678397
Chromosome Location	chr11:66324583-66324584
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
ENSG00000248746	Chromatin interaction
ENSG00000174165	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

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];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12577111	0.83[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs12805133	0.85[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];0.81[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs1671063	0.86[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs1671064	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[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];0.80[CHD][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	0.91[ASW][hapmap];0.92[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];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2000939	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276138	0.83[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs2279863	0.90[JPT][hapmap]
rs3018318	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741363	0.83[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs486584	1.00[CHB][hapmap];0.83[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	0.92[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];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs531490	0.94[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	0.92[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];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs545009	0.97[AMR][1000 genomes];0.99[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	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs572846	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[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	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618838	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs630021	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs677488	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];0.81[CHD][hapmap];0.90[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs678397	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs678397	CCS	cis	multi-tissue	Pritchard
rs678397	ACTN3	cis	Artery Aorta	GTEx
rs678397	ACTN3	cis	Muscle Skeletal	GTEx
rs678397	CCS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 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	chr11:66321600-66324600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:66321800-66326400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr11:66321800-66326400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:66321800-66326400	Weak transcription	Gastric	stomach
13	chr11:66322200-66325800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:66322600-66331400	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr11:66323000-66324600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:66323000-66325400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:66323600-66326400	Weak transcription	Pancreas	Pancrea
18	chr11:66323800-66324800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr11:66323800-66325000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:66323800-66325000	Weak transcription	Fetal Muscle Leg	muscle
21	chr11:66324400-66325200	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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