Variant report

Variant	rs17496586
Chromosome Location	chr11:66315512-66315513
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:66315380-66315530	A549	lung:	n/a	n/a
2	CTCF	chr11:66315460-66315610	NHDF-neo	bronchial:	n/a	chr11:66315546-66315559
3	CTCF	chr11:66315500-66315650	HepG2	liver:	n/a	chr11:66315546-66315559
4	CTCF	chr11:66315420-66315570	GM12865	blood:	n/a	chr11:66315546-66315559
5	MAFK	chr11:66315071-66315650	H1-hESC	embryonic stem cell:	n/a	chr11:66315275-66315289 chr11:66315276-66315286 chr11:66315274-66315290 chr11:66315271-66315286 chr11:66315272-66315292
6	CTCF	chr11:66315460-66315610	Hela-S3	cervix:	n/a	chr11:66315546-66315559
7	CTCF	chr11:66315486-66315540	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr11:66315380-66315530	GM12871	blood:	n/a	n/a
9	YY1	chr11:66315016-66315522	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr11:66315500-66315650	MCF-7	breast:	n/a	chr11:66315546-66315559

No.	Distal block	Cell Line	Cell type
1	chr11:66313928..66316895-chr11:66444565..66446585,2	K562	blood:
2	chr11:66312120..66315858-chr11:66382093..66385516,4	K562	blood:
3	chr11:66311475..66316022-chr11:66335981..66338223,4	MCF-7	breast:
4	chr11:66246144..66249538-chr11:66312277..66316497,5	MCF-7	breast:
5	chr11:66276681..66279418-chr11:66315413..66317207,2	MCF-7	breast:
6	chr11:66312923..66315636-chr11:66381243..66385459,4	MCF-7	breast:
7	chr11:66311617..66317579-chr11:66325496..66333927,8	MCF-7	breast:
8	chr11:66312879..66315564-chr11:66382748..66385471,3	MCF-7	breast:
9	chr11:66313372..66315858-chr11:66382227..66384523,2	K562	blood:

Variant related genes	Relation type
ZDHHC24	TF binding region
ENSG00000248643	Chromatin interaction
ENSG00000255517	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000174483	Chromatin interaction
ENSG00000199325	Chromatin interaction
ENSG00000254986	Chromatin interaction
ENSG00000174080	Chromatin interaction
ENSG00000250105	Chromatin interaction
ENSG00000173914	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10501397	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10896124	0.93[EUR][1000 genomes]
rs10896125	0.95[EUR][1000 genomes]
rs10896129	0.95[EUR][1000 genomes]
rs11227495	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11227497	0.95[EUR][1000 genomes]
rs11227498	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11227499	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11227500	0.95[EUR][1000 genomes]
rs11227501	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11227502	0.95[EUR][1000 genomes]
rs11227503	0.95[EUR][1000 genomes]
rs11227509	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11227510	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11227511	0.95[EUR][1000 genomes]
rs11227512	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11227514	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11227515	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11227522	0.87[EUR][1000 genomes]
rs11227523	0.97[EUR][1000 genomes]
rs11227525	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11227527	0.97[EUR][1000 genomes]
rs11227534	0.95[EUR][1000 genomes]
rs11550299	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11821155	0.89[EUR][1000 genomes]
rs11822028	0.95[EUR][1000 genomes]
rs11822099	0.95[EUR][1000 genomes]
rs11824771	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12099041	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12221821	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12223479	0.85[EUR][1000 genomes]
rs12272545	0.93[EUR][1000 genomes]
rs17065	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17147644	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17496250	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17580784	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2075792	0.95[EUR][1000 genomes]
rs2276406	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2277302	0.89[EUR][1000 genomes]
rs2279864	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2279865	0.82[EUR][1000 genomes]
rs2298806	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2305532	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2305533	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2305534	0.95[EUR][1000 genomes]
rs2305535	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28414721	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3179961	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35733139	0.86[EUR][1000 genomes]
rs3737525	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3741360	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3816492	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3819247	0.95[EUR][1000 genomes]
rs3825065	0.97[EUR][1000 genomes]
rs3892818	0.89[EUR][1000 genomes]
rs4542420	0.95[EUR][1000 genomes]
rs4576	0.95[EUR][1000 genomes]
rs4630309	0.95[EUR][1000 genomes]
rs4930182	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4930183	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4930377	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4930378	0.91[EUR][1000 genomes]
rs4930379	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4930380	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56144989	0.94[EUR][1000 genomes]
rs57045447	0.95[EUR][1000 genomes]
rs57207756	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57288351	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57596493	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57634456	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57691879	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57724777	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59829960	0.95[EUR][1000 genomes]
rs59982644	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60358007	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60645853	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61561111	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61582507	0.85[EUR][1000 genomes]
rs7104378	0.82[EUR][1000 genomes]
rs7116921	0.97[EUR][1000 genomes]
rs7116940	0.95[EUR][1000 genomes]
rs7123176	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7928882	0.86[EUR][1000 genomes]
rs7939759	0.95[EUR][1000 genomes]
rs7943327	0.91[EUR][1000 genomes]
rs7950407	0.92[EUR][1000 genomes]
rs7950790	0.81[AMR][1000 genomes];0.92[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17496586	CCS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66312800-66316000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr11:66313800-66315600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr11:66314000-66315800	Weak transcription	HSMMtube	muscle
4	chr11:66314200-66315600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:66314200-66315600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:66314200-66316600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:66314200-66321400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:66314400-66316200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:66314400-66316400	Weak transcription	Lung	lung
10	chr11:66314400-66320400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr11:66314400-66327000	Weak transcription	Right Atrium	heart
12	chr11:66314600-66316200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr11:66314600-66317000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr11:66314800-66315600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:66314800-66315600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr11:66314800-66315600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:66314800-66315600	Flanking Active TSS	Fetal Muscle Leg	muscle
18	chr11:66314800-66315800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:66314800-66316000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:66314800-66316800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:66314800-66326600	Weak transcription	Psoas Muscle	Psoas
22	chr11:66315000-66315600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr11:66315000-66315600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr11:66315000-66316800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr11:66315200-66315600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
26	chr11:66315200-66315600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr11:66315200-66315600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:66315200-66317000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr11:66315400-66316200	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr11:66315400-66316200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:66315400-66316200	Enhancers	HepG2	liver
32	chr11:66315400-66316400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr11:66315400-66316800	Flanking Active TSS	Fetal Muscle Trunk	muscle
34	chr11:66315400-66323600	Weak transcription	H9 Cell Line	embryonic stem cell

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