Variant report

Variant	rs3741370
Chromosome Location	chr11:65989758-65989759
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65983052..65986048-chr11:65987938..65993154,6	K562	blood:
2	chr11:65989212..65991575-chr11:66026106..66027836,2	K562	blood:
3	chr11:65987811..65990997-chr11:66051307..66054931,3	MCF-7	breast:
4	chr11:65989443..65990830-chr11:66049701..66050885,7	MCF-7	breast:
5	chr11:65985101..65987489-chr11:65988422..65991212,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174851	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000174871	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11823726	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12419425	0.82[ASN][1000 genomes]
rs12420458	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12803276	1.00[GIH][hapmap]
rs17147325	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs17147371	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs17307346	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1893316	1.00[GIH][hapmap]
rs2282567	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2452680	1.00[GIH][hapmap]
rs3782081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862387	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4930337	0.86[CHB][hapmap]
rs4930340	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs55835736	0.87[ASN][1000 genomes]
rs55944083	0.82[ASN][1000 genomes]
rs56269595	0.82[ASN][1000 genomes]
rs57579741	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61890288	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61890290	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61891385	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61891827	0.85[ASN][1000 genomes]
rs873491	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.84[ASN][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	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3741370	INCENP	cis	cerebellum	SCAN
rs3741370	SF3B2	cis	cerebellum	SCAN
rs3741370	FERMT3	cis	parietal	SCAN
rs3741370	SLC22A6	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65961400-66011200	Weak transcription	Psoas Muscle	Psoas
2	chr11:65976600-66006000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:65976800-65996000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr11:65977000-65989800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr11:65977200-65996000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:65977400-65990000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:65977400-66010600	Strong transcription	Fetal Stomach	stomach
8	chr11:65977600-65989800	Strong transcription	Fetal Intestine Small	intestine
9	chr11:65977600-66018600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:65977800-65989800	Strong transcription	Primary T cells from cord blood	blood
11	chr11:65977800-65990000	Strong transcription	Fetal Muscle Leg	muscle
12	chr11:65978000-65989800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:65978000-65993000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr11:65978800-65989800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:65979600-65989800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr11:65979800-66001200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:65980000-65994000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:65981200-65990200	Weak transcription	Fetal Kidney	kidney
19	chr11:65982200-65995800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr11:65982800-65989800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr11:65982800-65989800	Strong transcription	Thymus	Thymus
22	chr11:65982800-65989800	Strong transcription	Spleen	Spleen
23	chr11:65982800-65990000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr11:65983400-65989800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:65983400-65990000	Strong transcription	Gastric	stomach
26	chr11:65983400-65990200	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:65983600-65989800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr11:65984200-65989800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:65984600-66024200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:65984800-65991000	Weak transcription	Fetal Brain Male	brain
31	chr11:65984800-66000400	Weak transcription	HMEC	breast
32	chr11:65985200-65998800	Weak transcription	NHDF-Ad	bronchial
33	chr11:65985600-65989800	Weak transcription	HepG2	liver
34	chr11:65985600-65990000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:65985600-65991000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:65985800-65990200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr11:65985800-65991800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:65985800-66017800	Weak transcription	Fetal Heart	heart
39	chr11:65986600-65991800	Weak transcription	NH-A	brain
40	chr11:65987000-65992200	Weak transcription	HSMMtube	muscle
41	chr11:65987600-65992200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr11:65987800-65990000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr11:65987800-65990000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:65987800-65991800	Weak transcription	HSMM	muscle
45	chr11:65987800-66003400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:65988000-65989800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr11:65988200-65989800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr11:65988200-65991800	Weak transcription	Colon Smooth Muscle	Colon
49	chr11:65988200-66001200	Weak transcription	Small Intestine	intestine
50	chr11:65988400-65992400	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links