Variant report

Variant	rs731384
Chromosome Location	chr11:57408382-57408383
allele	C/T
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	POLR2A	chr11:57406679-57409638	PBDE	blood:	n/a	n/a
2	CTCF	chr11:57408240-57408390	HVMF	connective:	n/a	n/a
3	CTCF	chr11:57408348-57409387	K562	blood:	n/a	chr11:57409157-57409178 chr11:57409163-57409179 chr11:57409162-57409180
4	POLR2A	chr11:57404829-57418710	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr11:57404853-57409799	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr11:57404978-57410762	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:57404927-57409727	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr11:57408232-57409596	A549	lung:	n/a	chr11:57409157-57409178 chr11:57409163-57409179 chr11:57409162-57409180
9	POLR2A	chr11:57404802-57417187	SK-N-MC	brain:	n/a	n/a
10	ATF2	chr11:57408370-57409591	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr11:57408367-57409579	HCT-116	colon:	n/a	chr11:57409157-57409178 chr11:57409163-57409179 chr11:57409162-57409180
12	POLR2A	chr11:57405031-57409669	PFSK-1	brain:	n/a	n/a
13	CTCF	chr11:57408300-57408450	GM12866	blood:	n/a	n/a
14	CTCF	chr11:57408341-57409607	SK-N-SH	brain:	n/a	chr11:57409157-57409178 chr11:57409163-57409179 chr11:57409162-57409180
15	CTCF	chr11:57408340-57408490	GM06990	blood:	n/a	n/a
16	POLR2A	chr11:57407849-57408546	H1-hESC	embryonic stem cell:	n/a	n/a
17	SMC3	chr11:57408359-57409756	SK-N-SH	brain:	n/a	chr11:57409164-57409178
18	POLR2A	chr11:57404949-57409673	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr11:57408280-57408430	GM12868	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57335324..57336323-chr11:57408291..57409695,14	MCF-7	breast:
2	chr11:57405566..57408530-chr11:57408605..57410550,2	MCF-7	breast:
3	chr11:57407680..57409367-chr11:57422916..57424875,2	MCF-7	breast:
4	chr11:57334539..57338384-chr11:57406664..57411574,5	MCF-7	breast:

Variant related genes	Relation type
MIR130A	TF binding region
ENSG00000208009	Chromatin interaction
ENSG00000156587	Chromatin interaction
ENSG00000172409	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10750866	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10896631	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10896632	0.83[ASN][1000 genomes]
rs10896633	1.00[ASW][hapmap];0.81[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10896636	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11229063	0.86[AFR][1000 genomes]
rs11229066	1.00[JPT][hapmap];0.86[AFR][1000 genomes]
rs11229067	1.00[ASW][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[AFR][1000 genomes]
rs11229075	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11229077	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11229078	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11229080	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11570190	0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs11570195	0.90[LWK][hapmap]
rs11602109	0.86[AFR][1000 genomes]
rs11603020	1.00[ASW][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.86[AFR][1000 genomes]
rs11604325	0.81[AFR][1000 genomes]
rs11604333	0.81[AFR][1000 genomes]
rs11605731	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11606396	0.86[AFR][1000 genomes]
rs11606677	1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11606706	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11607056	0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs12146541	0.81[AFR][1000 genomes]
rs12362166	0.86[AFR][1000 genomes]
rs12785533	0.81[AFR][1000 genomes]
rs12804972	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12805841	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12807250	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1647395	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1647405	0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs2081361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28362934	0.90[CHD][hapmap]
rs28362947	0.86[AFR][1000 genomes]
rs28362948	0.86[AFR][1000 genomes]
rs28362949	0.86[AFR][1000 genomes]
rs28362951	0.86[AFR][1000 genomes]
rs2847308	0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs34052104	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3758919	0.90[CHD][hapmap]
rs3824988	1.00[ASW][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];0.86[AFR][1000 genomes]
rs4827	0.81[AFR][1000 genomes]
rs4926	1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs499188	0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs55649513	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55920079	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs576859	0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs708228	0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs7102271	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7116341	0.81[AFR][1000 genomes]
rs7117878	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7117896	0.81[ASN][1000 genomes]
rs7121169	0.86[AFR][1000 genomes]
rs71484461	0.81[AFR][1000 genomes]
rs73480556	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73480560	0.80[EUR][1000 genomes]
rs7938083	0.81[AFR][1000 genomes]
rs9420	0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	esv992553	chr11:57408294-57419351	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs731384	MS4A7	cis	cerebellum	SCAN
rs731384	OR4D11	cis	parietal	SCAN
rs731384	MED19	cis	cerebellum	SCAN
rs731384	TIMM10	cis	parietal	SCAN
rs731384	OR1S1	cis	cerebellum	SCAN
rs731384	OR8J1	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57403000-57412200	Weak transcription	Hela-S3	cervix
2	chr11:57405000-57408800	Active TSS	Fetal Kidney	kidney
3	chr11:57406200-57408400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:57406400-57409000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr11:57406600-57409000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:57406600-57409000	Enhancers	K562	blood
7	chr11:57406800-57408400	Flanking Active TSS	HepG2	liver
8	chr11:57406800-57408600	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr11:57406800-57408600	Weak transcription	Brain Substantia Nigra	brain
10	chr11:57406800-57408800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:57406800-57408800	Flanking Active TSS	Fetal Brain Female	brain
12	chr11:57406800-57409600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:57407000-57408800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr11:57407000-57408800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr11:57407000-57408800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:57407000-57409200	Enhancers	Liver	Liver
17	chr11:57407200-57408400	Flanking Active TSS	HSMM	muscle
18	chr11:57407200-57408800	Enhancers	Left Ventricle	heart
19	chr11:57407200-57408800	Genic enhancers	Right Atrium	heart
20	chr11:57407200-57409000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
21	chr11:57407200-57409000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
22	chr11:57407200-57409400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
23	chr11:57407200-57409400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
24	chr11:57407200-57412200	Weak transcription	Ovary	ovary
25	chr11:57407400-57408400	Flanking Active TSS	Fetal Brain Male	brain
26	chr11:57407400-57408400	Enhancers	Rectal Smooth Muscle	rectum
27	chr11:57407400-57408600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:57407400-57408600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr11:57407400-57408600	Flanking Active TSS	NHLF	lung
30	chr11:57407400-57408800	Enhancers	Adipose Nuclei	Adipose
31	chr11:57407400-57408800	Enhancers	Brain Hippocampus Middle	brain
32	chr11:57407400-57408800	Enhancers	Placenta	Placenta
33	chr11:57407400-57409000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:57407400-57412600	Weak transcription	GM12878-XiMat	blood
35	chr11:57407600-57408800	Enhancers	Placenta Amnion	Placenta Amnion
36	chr11:57407600-57408800	Enhancers	Thymus	Thymus
37	chr11:57407600-57409000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:57407600-57409000	Enhancers	Brain Anterior Caudate	brain
39	chr11:57407600-57409000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr11:57407600-57409200	Enhancers	Primary T cells from cord blood	blood
41	chr11:57407600-57409200	Weak transcription	Colonic Mucosa	Colon
42	chr11:57407600-57409200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr11:57407600-57412200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr11:57407600-57412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr11:57407600-57412200	Weak transcription	Spleen	Spleen
46	chr11:57407600-57413000	Weak transcription	Right Ventricle	heart
47	chr11:57407600-57413200	Weak transcription	Esophagus	oesophagus
48	chr11:57407800-57408400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:57407800-57408800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:57407800-57408800	Enhancers	Stomach Smooth Muscle	stomach

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