Variant report

Variant	rs540874
Chromosome Location	chr11:66329732-66329733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66329301-66329799	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66328699..66330263-chr11:66360114..66361781,2	K562	blood:
2	chr11:66328947..66331714-chr11:66414609..66416864,2	K562	blood:
3	chr11:66311617..66317579-chr11:66325496..66333927,8	MCF-7	breast:
4	chr11:66329216..66333273-chr11:66381522..66384587,4	K562	blood:
5	chr11:66323180..66325641-chr11:66328411..66330736,2	MCF-7	breast:
6	chr11:66327944..66330725-chr11:66391381..66393880,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000250105	TF binding region
ENSG00000248643	Chromatin interaction
ENSG00000182791	Chromatin interaction
ENSG00000248746	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000199325	Chromatin interaction
ENSG00000174165	Chromatin interaction
ENSG00000173992	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs10736656	0.85[ASN][1000 genomes]
rs10791882	0.94[ASN][1000 genomes]
rs1127894	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12577111	0.83[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs12805133	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs1671062	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs1671063	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs1671064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1671065	0.85[ASN][1000 genomes]
rs1700189	0.82[ASN][1000 genomes]
rs1791684	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.83[ASN][1000 genomes]
rs1791686	0.86[ASN][1000 genomes]
rs1815739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2000939	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276138	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs2279863	0.90[JPT][hapmap]
rs3018318	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3741363	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs486584	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs4930387	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs503250	0.83[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.81[ASN][1000 genomes]
rs508443	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs509556	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];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531490	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs535211	0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap]
rs545009	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556759	0.83[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.81[ASN][1000 genomes]
rs560556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs566673	0.82[GIH][hapmap]
rs572846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577023	0.95[JPT][hapmap]
rs580910	0.91[JPT][hapmap];0.83[MEX][hapmap]
rs615205	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618838	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs630021	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs677488	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]
rs678397	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]
rs692892	0.83[CHB][hapmap]
rs7925108	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs8432	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs540874	KDM2A	cis	cerebellum	SCAN
rs540874	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs540874	CCS	cis	lymphoblastoid	seeQTL
rs540874	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs540874	PRDX5	cis	cerebellum	SCAN
rs540874	UNC93B1	cis	cerebellum	SCAN
rs540874	ACTN3	cis	Muscle Skeletal	GTEx
rs540874	CTSF	cis	parietal	SCAN
rs540874	CDC42EP2	cis	cerebellum	SCAN
rs540874	YIF1A	cis	cerebellum	SCAN
rs540874	ACTN3	cis	Artery Aorta	GTEx
rs540874	ACTN3	cis	lymphoblastoid	seeQTL
rs540874	GANAB	cis	parietal	SCAN
rs540874	SYT12	cis	parietal	SCAN
rs540874	CCDC85B	cis	parietal	SCAN
rs540874	YIF1A	cis	parietal	SCAN
rs540874	CCS	cis	multi-tissue	Pritchard
rs540874	CTSF	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66319000-66337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:66321400-66330400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:66321400-66331600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:66322600-66331400	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr11:66326600-66331800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:66326600-66334800	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:66326800-66329800	Weak transcription	Brain Anterior Caudate	brain
8	chr11:66326800-66329800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:66326800-66329800	Weak transcription	Fetal Brain Female	brain
10	chr11:66326800-66331200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:66326800-66331200	Weak transcription	Right Ventricle	heart
12	chr11:66326800-66331400	Weak transcription	Liver	Liver
13	chr11:66326800-66334800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr11:66326800-66334800	Weak transcription	Pancreas	Pancrea
15	chr11:66326800-66335000	Weak transcription	Psoas Muscle	Psoas
16	chr11:66326800-66335000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr11:66326800-66335200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:66326800-66335200	Weak transcription	Esophagus	oesophagus
19	chr11:66326800-66335200	Weak transcription	Left Ventricle	heart
20	chr11:66326800-66335200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:66327000-66330400	Weak transcription	Ovary	ovary
22	chr11:66327000-66332600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr11:66327000-66333000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:66327000-66335200	Weak transcription	Fetal Heart	heart
25	chr11:66327200-66330400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr11:66327200-66330800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:66327200-66332200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:66327200-66333200	Weak transcription	Lung	lung
29	chr11:66327200-66335000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr11:66327400-66331800	Weak transcription	Placenta	Placenta
31	chr11:66327400-66334600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr11:66327400-66335200	Weak transcription	Right Atrium	heart
33	chr11:66327600-66330400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr11:66327600-66332200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr11:66327800-66330400	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr11:66327800-66330600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr11:66327800-66331200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr11:66327800-66332000	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr11:66328000-66333000	Strong transcription	Fetal Muscle Leg	muscle
40	chr11:66328000-66334000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr11:66328000-66334400	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr11:66328000-66335000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:66328200-66331800	Weak transcription	Gastric	stomach
44	chr11:66328200-66333600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr11:66328400-66330600	Weak transcription	Spleen	Spleen
46	chr11:66328400-66334800	Strong transcription	Fetal Stomach	stomach
47	chr11:66329000-66329800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:66329000-66331200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:66329000-66334200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:66329000-66334600	Strong transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links