Variant report

Variant	rs3133327
Chromosome Location	chr11:67854632-67854633
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:67853936..67856496-chr11:67886644..67889004,3	MCF-7	breast:
2	chr11:67848842..67850960-chr11:67853567..67855233,2	K562	blood:
3	chr11:67848510..67851097-chr11:67851129..67856478,5	K562	blood:

Variant related genes	Relation type
ENSG00000110721	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10791956	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10791957	0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10896293	0.81[EUR][1000 genomes]
rs10896298	0.81[MEX][hapmap]
rs11228129	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11228131	0.87[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11228137	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11228144	0.88[JPT][hapmap]
rs11228145	0.89[JPT][hapmap]
rs11535788	0.82[EUR][1000 genomes]
rs11824199	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1894204	0.80[MEX][hapmap]
rs2457179	0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2457180	0.82[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs2511437	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2511467	0.92[CEU][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes]
rs2511468	0.85[EUR][1000 genomes]
rs2511469	0.89[JPT][hapmap]
rs2511470	0.87[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.87[EUR][1000 genomes]
rs2511472	0.89[JPT][hapmap]
rs2511475	0.92[CEU][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2511478	0.85[EUR][1000 genomes]
rs2511479	0.92[CEU][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs2512608	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2512611	0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2512612	0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2512623	0.89[JPT][hapmap];0.90[MEX][hapmap]
rs2512624	0.90[EUR][1000 genomes]
rs3819255	0.96[CEU][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3935460	0.81[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4073551	0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4345973	0.81[MEX][hapmap]
rs4930227	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4930557	0.82[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs4930561	0.81[MEX][hapmap]
rs6591331	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7104982	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7123183	0.81[EUR][1000 genomes]
rs7123668	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7925022	0.82[EUR][1000 genomes]
rs7928739	0.82[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs7931502	0.81[MEX][hapmap]
rs7940217	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7940501	0.88[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs7944372	0.88[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427892	chr11:67451649-67926562	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	esv2757450	chr11:67472905-67891289	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	112 gene(s)	inside rSNPs	diseases
3	esv2759835	chr11:67472905-67891289	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	112 gene(s)	inside rSNPs	diseases
4	esv2758275	chr11:67524937-67859490	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
5	nsv469856	chr11:67639037-67859490	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
6	nsv482760	chr11:67639037-67859490	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
7	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3133327	SF1	cis	parietal	SCAN
rs3133327	SPDYC	cis	parietal	SCAN
rs3133327	FGF19	cis	parietal	SCAN
rs3133327	PACS1	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67812200-67875400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:67831400-67884400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:67831600-67867000	Weak transcription	Small Intestine	intestine
4	chr11:67833800-67858200	Weak transcription	HUVEC	blood vessel
5	chr11:67838000-67867000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:67838000-67879200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:67838400-67858200	Weak transcription	NH-A	brain
8	chr11:67838600-67864400	Weak transcription	Osteobl	bone
9	chr11:67839200-67870600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:67839800-67873200	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:67839800-67886000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:67842400-67858200	Weak transcription	Fetal Thymus	thymus
13	chr11:67842400-67859000	Weak transcription	HSMMtube	muscle
14	chr11:67842400-67867000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:67845600-67857200	Weak transcription	A549	lung
16	chr11:67846000-67858200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr11:67846200-67857600	Weak transcription	Fetal Heart	heart
18	chr11:67846200-67867000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:67846400-67856800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr11:67848400-67886400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:67848600-67857400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:67848800-67859200	Weak transcription	Aorta	Aorta
23	chr11:67848800-67861400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:67848800-67865800	Weak transcription	K562	blood
25	chr11:67848800-67866200	Weak transcription	Right Ventricle	heart
26	chr11:67848800-67867000	Weak transcription	Placenta	Placenta
27	chr11:67848800-67874200	Weak transcription	Colonic Mucosa	Colon
28	chr11:67849000-67856600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr11:67849000-67857200	Weak transcription	Lung	lung
30	chr11:67849000-67866400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:67849000-67866800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr11:67849000-67867000	Weak transcription	Ovary	ovary
33	chr11:67849000-67885400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr11:67849200-67856600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr11:67849200-67856600	Weak transcription	Brain Substantia Nigra	brain
36	chr11:67849200-67857200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr11:67849200-67857600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr11:67849200-67857600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:67849200-67857800	Weak transcription	Adipose Nuclei	Adipose
40	chr11:67849200-67858200	Weak transcription	HSMM	muscle
41	chr11:67849200-67867000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:67849400-67856600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:67849400-67856600	Weak transcription	Dnd41	blood
44	chr11:67849400-67856800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr11:67849400-67857400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:67849400-67857400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr11:67849400-67858000	Weak transcription	Primary T cells from cord blood	blood
48	chr11:67849400-67858200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:67849400-67860000	Weak transcription	Fetal Muscle Leg	muscle
50	chr11:67849400-67861400	Weak transcription	Hela-S3	cervix

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