Variant report

Variant	rs4909945
Chromosome Location	chr11:10673739-10673740
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	TCF7L2	chr11:10673168-10673806	HCT-116	colon:	n/a	n/a
2	YY1	chr11:10673577-10673915	HCT-116	colon:	n/a	n/a
3	POLR2A	chr11:10673173-10673807	HCT-116	colon:	n/a	n/a
4	MAX	chr11:10673139-10674070	HCT-116	colon:	n/a	chr11:10673554-10673564 chr11:10673832-10673841
5	NFIC	chr11:10673259-10673861	ECC-1	luminal epithelium:	n/a	chr11:10673525-10673542 chr11:10673525-10673541
6	USF1	chr11:10673123-10674040	HCT-116	colon:	n/a	n/a
7	MAX	chr11:10673093-10674150	HCT-116	colon:	n/a	chr11:10673554-10673564 chr11:10673832-10673841

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:10322610..10325546-chr11:10673380..10676333,2	K562	blood:
2	chr11:10560102..10563921-chr11:10672313..10677222,4	MCF-7	breast:

Variant related genes	Relation type
MRVI1	TF binding region
ENSG00000254554	Chromatin interaction
ENSG00000177112	Chromatin interaction
ENSG00000110315	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1035691	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10840453	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042902	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11042906	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603178	1.00[JPT][hapmap]
rs1462940	1.00[JPT][hapmap]
rs1544861	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16908001	1.00[JPT][hapmap]
rs16927077	1.00[JPT][hapmap]
rs17318955	1.00[JPT][hapmap]
rs17403439	1.00[JPT][hapmap]
rs17403460	1.00[JPT][hapmap]
rs17403795	1.00[JPT][hapmap]
rs17403942	1.00[JPT][hapmap]
rs17403977	1.00[JPT][hapmap]
rs1863243	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863244	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1979367	1.00[JPT][hapmap]
rs2052690	0.88[AMR][1000 genomes]
rs2052691	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052692	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2098839	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4025	1.00[JPT][hapmap]
rs41464450	1.00[JPT][hapmap]
rs4442541	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910160	1.00[JPT][hapmap]
rs4910165	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6484437	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7936275	0.82[AMR][1000 genomes]
rs7940646	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881869	1.00[JPT][hapmap]
rs903822	1.00[JPT][hapmap]
rs903823	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv832063	chr11:10618485-10785281	ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Migraine	23793025	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4909945	STK33	cis	parietal	SCAN
rs4909945	USP47	cis	cerebellum	SCAN
rs4909945	SPON1	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10646000-10679000	Weak transcription	Fetal Lung	lung
2	chr11:10646200-10679200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr11:10650400-10678600	Weak transcription	Right Ventricle	heart
4	chr11:10658800-10676600	Enhancers	Primary B cells from peripheral blood	blood
5	chr11:10664200-10678800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:10664400-10675000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr11:10668400-10673800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:10668600-10674200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:10668600-10674400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr11:10668800-10674200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr11:10669400-10674400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr11:10669600-10675600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:10669600-10676800	Weak transcription	Fetal Intestine Large	intestine
14	chr11:10670200-10674600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr11:10670200-10675000	Weak transcription	K562	blood
16	chr11:10670400-10675400	Genic enhancers	Fetal Stomach	stomach
17	chr11:10670800-10675000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:10670800-10676400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:10671000-10676200	Weak transcription	A549	lung
20	chr11:10671400-10676000	Enhancers	Brain Anterior Caudate	brain
21	chr11:10671400-10676200	Enhancers	Brain Hippocampus Middle	brain
22	chr11:10671400-10677000	Weak transcription	Fetal Intestine Small	intestine
23	chr11:10672000-10679200	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr11:10672200-10674600	Weak transcription	Primary B cells from cord blood	blood
25	chr11:10672400-10674400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:10672400-10674400	Weak transcription	Fetal Muscle Leg	muscle
27	chr11:10672400-10675000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:10672600-10674400	Weak transcription	Brain Angular Gyrus	brain
29	chr11:10672600-10674400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr11:10672600-10674800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:10672800-10674000	Weak transcription	Brain Substantia Nigra	brain
32	chr11:10673000-10682200	Enhancers	Placenta	Placenta
33	chr11:10673200-10673800	Enhancers	Osteobl	bone
34	chr11:10673200-10674000	Enhancers	NH-A	brain
35	chr11:10673200-10674600	Enhancers	NHDF-Ad	bronchial
36	chr11:10673200-10675800	Enhancers	Lung	lung
37	chr11:10673200-10676200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:10673200-10676800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr11:10673200-10677800	Enhancers	Colon Smooth Muscle	Colon
40	chr11:10673400-10673800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr11:10673400-10673800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr11:10673400-10673800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:10673400-10673800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:10673400-10673800	Enhancers	Aorta	Aorta
45	chr11:10673400-10674000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:10673400-10674000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:10673400-10674000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:10673400-10674000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:10673400-10674000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:10673400-10674000	Enhancers	Sigmoid Colon	Sigmoid Colon

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