Variant report

Variant	rs11733177
Chromosome Location	chr4:7931249-7931250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7930429..7933293-chr4:7935968..7937557,2	MCF-7	breast:
2	chr4:7930761..7932557-chr4:7940188..7942388,2	MCF-7	breast:
3	chr4:7805890..7806402-chr4:7930617..7931480,2	MCF-7	breast:
4	chr4:7877287..7878806-chr4:7930542..7931312,4	MCF-7	breast:
5	chr4:7845826..7846609-chr4:7930534..7931357,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228919	Chromatin interaction
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11733297	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs11930623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500566	1.00[CHB][hapmap]
rs12509421	0.81[CEU][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs13124202	1.00[CHB][hapmap]
rs13137827	1.00[CHB][hapmap]
rs16840961	1.00[CHB][hapmap]
rs17177036	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs17177064	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs17770213	0.86[TSI][hapmap]
rs17770321	0.80[TSI][hapmap]
rs17771470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17832709	0.86[TSI][hapmap]
rs28622214	0.86[TSI][hapmap]
rs55767717	0.82[AMR][1000 genomes]
rs55938116	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56078222	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62290601	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6813758	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs6829680	0.89[TSI][hapmap]
rs73214051	0.82[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	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11733177	MSX1	cis	cerebellum	SCAN
rs11733177	AFAP1	cis	Whole Blood	GTEx
rs11733177	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs11733177	AFAP1	cis	cerebellum	SCAN
rs11733177	AFAP	cis	multi-tissue	Pritchard
rs11733177	ABLIM2	cis	cerebellum	SCAN
rs11733177	AFAP1	cis	Esophagus Mucosa	GTEx
rs11733177	STX18	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
2	chr4:7923000-7931600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:7926600-7936600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:7926800-7935400	Weak transcription	Fetal Brain Male	brain
5	chr4:7927800-7932400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr4:7928000-7932000	Enhancers	Stomach Mucosa	stomach
7	chr4:7928200-7932200	Enhancers	Colon Smooth Muscle	Colon
8	chr4:7929200-7931400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:7930000-7932000	Genic enhancers	Fetal Stomach	stomach
10	chr4:7930400-7931400	Enhancers	Stomach Smooth Muscle	stomach
11	chr4:7930400-7932000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:7930400-7932000	Genic enhancers	Fetal Lung	lung
13	chr4:7930400-7932200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:7930400-7932200	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr4:7930400-7932400	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr4:7930400-7934000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:7930600-7931400	Enhancers	Fetal Brain Female	brain
18	chr4:7930600-7931600	Enhancers	HepG2	liver
19	chr4:7930600-7931800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:7930600-7931800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr4:7930600-7931800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:7930600-7931800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:7930600-7931800	Enhancers	Adipose Nuclei	Adipose
24	chr4:7930600-7931800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr4:7930600-7932000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:7930600-7932000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:7930600-7932000	Enhancers	Brain Anterior Caudate	brain
28	chr4:7930600-7932000	Enhancers	Duodenum Mucosa	Duodenum
29	chr4:7930600-7932000	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr4:7930600-7932000	Enhancers	HSMMtube	muscle
31	chr4:7930600-7932200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr4:7930600-7932200	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr4:7930600-7932200	Enhancers	Colonic Mucosa	Colon
34	chr4:7930600-7932200	Enhancers	Fetal Muscle Leg	muscle
35	chr4:7930600-7932200	Enhancers	Pancreas	Pancrea
36	chr4:7930600-7932200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr4:7930600-7932200	Enhancers	HSMM	muscle
38	chr4:7930600-7932400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:7930600-7932400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr4:7930600-7932400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:7930600-7932400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:7930600-7932400	Enhancers	Esophagus	oesophagus
43	chr4:7930600-7932600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr4:7930600-7932600	Enhancers	Placenta	Placenta
45	chr4:7930600-7935600	Genic enhancers	Osteobl	bone
46	chr4:7930800-7931400	Genic enhancers	Fetal Intestine Small	intestine
47	chr4:7930800-7931400	Enhancers	Fetal Kidney	kidney
48	chr4:7930800-7931600	Enhancers	Brain Hippocampus Middle	brain
49	chr4:7930800-7931600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr4:7930800-7932000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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