Variant report

Variant	rs2078069
Chromosome Location	chr11:66038309-66038310
allele	A/C
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	WRNIP1	chr11:66038255-66038381	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65624882..65627968-chr11:66034504..66038316,6	K562	blood:
2	chr11:66034858..66038328-chr11:66053749..66060447,9	MCF-7	breast:
3	chr11:66034813..66037719-chr11:66037930..66039835,3	MCF-7	breast:
4	chr11:66036265..66039186-chr11:66074799..66077052,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254762	TF binding region
ENSG00000172732	Chromatin interaction
ENSG00000174851	Chromatin interaction
ENSG00000174903	Chromatin interaction
ENSG00000179292	Chromatin interaction
ENSG00000254762	Chromatin interaction
ENSG00000172757	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs3814739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs484261	0.96[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs4930173	0.88[ASN][1000 genomes]
rs4930344	0.88[ASN][1000 genomes]
rs4930345	0.89[ASN][1000 genomes]
rs4930346	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs513474	0.86[ASN][1000 genomes]
rs526200	0.81[ASN][1000 genomes]
rs534489	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs55746937	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55838040	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55931871	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56038054	0.87[ASN][1000 genomes]
rs561373	0.83[ASN][1000 genomes]
rs56151197	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56285664	0.84[ASN][1000 genomes]
rs57678007	0.88[ASN][1000 genomes]
rs7123153	0.86[ASN][1000 genomes]
rs7128537	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72936632	0.86[ASN][1000 genomes]
rs72936635	0.86[ASN][1000 genomes]
rs72936656	0.88[ASN][1000 genomes]
rs72936660	0.89[ASN][1000 genomes]
rs72936672	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72936699	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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	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
3	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
4	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
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2078069	C1orf223	trans	parietal	SCAN
rs2078069	FKBP2	cis	parietal	SCAN
rs2078069	C11orf83	cis	cerebellum	SCAN
rs2078069	SLC22A12	cis	parietal	SCAN
rs2078069	SNX32	cis	parietal	SCAN
rs2078069	UBXN1	cis	cerebellum	SCAN
rs2078069	SNX32	cis	cerebellum	SCAN
rs2078069	RAB1B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66037000-66039400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:66037000-66039800	Weak transcription	Small Intestine	intestine
3	chr11:66037200-66038400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr11:66037200-66038400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr11:66037200-66038400	Enhancers	Fetal Heart	heart
6	chr11:66037200-66038400	Enhancers	Left Ventricle	heart
7	chr11:66037200-66038400	Enhancers	Psoas Muscle	Psoas
8	chr11:66037200-66038600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr11:66037200-66038600	Enhancers	Pancreas	Pancrea
10	chr11:66037200-66039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:66037200-66039400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:66037200-66039400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:66037200-66039400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:66037200-66039400	Weak transcription	Ovary	ovary
15	chr11:66037200-66039400	Weak transcription	HSMMtube	muscle
16	chr11:66037200-66039600	Weak transcription	Aorta	Aorta
17	chr11:66037200-66039800	Weak transcription	Fetal Kidney	kidney
18	chr11:66037400-66038400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr11:66037400-66038400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:66037400-66038400	Enhancers	Adipose Nuclei	Adipose
21	chr11:66037400-66038400	Enhancers	Brain Hippocampus Middle	brain
22	chr11:66037400-66038400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr11:66037400-66038400	Genic enhancers	Fetal Muscle Leg	muscle
24	chr11:66037400-66038600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr11:66037400-66038600	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr11:66037400-66038600	Enhancers	Colon Smooth Muscle	Colon
27	chr11:66037400-66038600	Genic enhancers	Placenta	Placenta
28	chr11:66037400-66039200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr11:66037400-66039200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:66037400-66044600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr11:66037400-66044800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr11:66037600-66038400	Genic enhancers	Muscle Satellite Cultured Cells	--
33	chr11:66037600-66038400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:66037600-66038400	Enhancers	Right Ventricle	heart
35	chr11:66037600-66038600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr11:66037600-66038600	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr11:66037600-66038600	Genic enhancers	Fetal Muscle Trunk	muscle
38	chr11:66037600-66038800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:66037600-66039000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr11:66037600-66039000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:66037600-66039000	Weak transcription	HUVEC	blood vessel
42	chr11:66037600-66039200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr11:66037600-66039200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:66037600-66039200	Weak transcription	Brain Angular Gyrus	brain
45	chr11:66037600-66039200	Weak transcription	Brain Germinal Matrix	brain
46	chr11:66037600-66039200	Weak transcription	Fetal Brain Female	brain
47	chr11:66037600-66039200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:66037600-66039400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr11:66037600-66039400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:66037600-66039400	Weak transcription	Fetal Brain Male	brain

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