Variant report

Variant	rs11733297
Chromosome Location	chr4:7928845-7928846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7919498..7922242-chr4:7928069..7929802,2	K562	blood:
2	chr4:7927907..7930041-chr4:7939500..7941812,2	K562	blood:
3	chr4:7926036..7929500-chr4:7940242..7942845,4	MCF-7	breast:
4	chr4:7924008..7927501-chr4:7928282..7930975,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction
ENSG00000228919	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11722163	0.92[ASN][1000 genomes]
rs11732100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733177	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs11735005	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11930623	0.81[CEU][hapmap];0.80[AMR][1000 genomes]
rs12509421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17177064	0.88[AFR][1000 genomes]
rs17770213	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs17770321	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs17771470	0.82[CEU][hapmap];0.80[AMR][1000 genomes]
rs17832709	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28437157	0.80[EUR][1000 genomes]
rs28622214	0.85[CEU][hapmap]
rs34310670	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55767717	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55844411	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56220381	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56229515	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289335	0.80[EUR][1000 genomes]
rs62289336	0.80[EUR][1000 genomes]
rs62289337	0.80[EUR][1000 genomes]
rs62290561	0.83[EUR][1000 genomes]
rs62290571	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62290573	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62290574	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62290579	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814887	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6815298	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6829680	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6850654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6855532	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73214041	0.83[EUR][1000 genomes]
rs73214042	0.81[AMR][1000 genomes];0.88[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11733297	AFAP1	cis	Whole Blood	GTEx
rs11733297	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs11733297	AFAP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
3	chr4:7912000-7931200	Weak transcription	Aorta	Aorta
4	chr4:7912800-7931200	Weak transcription	Gastric	stomach
5	chr4:7913000-7930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:7913000-7931000	Weak transcription	Fetal Intestine Large	intestine
7	chr4:7913600-7930400	Weak transcription	NHEK	skin
8	chr4:7914200-7930800	Weak transcription	Fetal Kidney	kidney
9	chr4:7915000-7930400	Weak transcription	Fetal Lung	lung
10	chr4:7918800-7930400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:7919000-7929000	Weak transcription	Brain Germinal Matrix	brain
12	chr4:7919200-7930600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:7919600-7930800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:7919800-7930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:7919800-7931200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:7920600-7931200	Weak transcription	Lung	lung
17	chr4:7921000-7930600	Weak transcription	Esophagus	oesophagus
18	chr4:7921200-7930600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:7923000-7931600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:7925600-7929000	Genic enhancers	Osteobl	bone
21	chr4:7926000-7931200	Weak transcription	NHDF-Ad	bronchial
22	chr4:7926200-7929200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:7926200-7930600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:7926200-7930600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:7926400-7930800	Weak transcription	Brain Hippocampus Middle	brain
26	chr4:7926400-7931200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:7926600-7930400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr4:7926600-7930600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:7926600-7930600	Weak transcription	Fetal Brain Female	brain
30	chr4:7926600-7930600	Weak transcription	Pancreas	Pancrea
31	chr4:7926600-7930800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr4:7926600-7936600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:7926800-7929800	Strong transcription	Fetal Stomach	stomach
34	chr4:7926800-7930400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr4:7926800-7931200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:7926800-7931200	Weak transcription	Right Atrium	heart
37	chr4:7926800-7931200	Weak transcription	NHLF	lung
38	chr4:7926800-7935400	Weak transcription	Fetal Brain Male	brain
39	chr4:7927000-7929000	Weak transcription	Fetal Intestine Small	intestine
40	chr4:7927000-7930400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr4:7927000-7930600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr4:7927000-7930600	Weak transcription	Placenta	Placenta
43	chr4:7927000-7930600	Weak transcription	Hela-S3	cervix
44	chr4:7927000-7930600	Weak transcription	HSMM	muscle
45	chr4:7927000-7931000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:7927000-7931200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr4:7927000-7931200	Weak transcription	Fetal Heart	heart
48	chr4:7927200-7930600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:7927200-7930600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:7927200-7930600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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