Variant report

Variant	rs12509421
Chromosome Location	chr4:7929512-7929513
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	chr4:7924008..7927501-chr4:7928282..7930975,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228919	Chromatin interaction
ENSG00000196526	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11722163	0.92[ASN][1000 genomes]
rs11732100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733177	0.81[CEU][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs11733297	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]
rs11735005	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11930623	0.81[CEU][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs17177036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17177064	0.82[AFR][1000 genomes]
rs17770213	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.81[ASN][1000 genomes]
rs17770321	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs17771470	0.81[CEU][hapmap]
rs17832709	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28622214	0.85[CEU][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs34310670	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55767717	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55844411	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56220381	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56229515	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62290561	0.82[EUR][1000 genomes]
rs62290571	0.83[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	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814887	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6815298	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6829680	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6850654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6855532	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73214041	0.82[EUR][1000 genomes]
rs73214042	0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12509421	AFAP1	cis	Whole Blood	GTEx
rs12509421	AFAP1	cis	Esophagus Mucosa	GTEx
rs12509421	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12509421	AFAP1	cis	cerebellum	SCAN

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	chr4:7919200-7930600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr4:7919600-7930800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:7919800-7930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:7919800-7931200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:7920600-7931200	Weak transcription	Lung	lung
16	chr4:7921000-7930600	Weak transcription	Esophagus	oesophagus
17	chr4:7921200-7930600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:7923000-7931600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:7926000-7931200	Weak transcription	NHDF-Ad	bronchial
20	chr4:7926200-7930600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:7926200-7930600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:7926400-7930800	Weak transcription	Brain Hippocampus Middle	brain
23	chr4:7926400-7931200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:7926600-7930400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr4:7926600-7930600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:7926600-7930600	Weak transcription	Fetal Brain Female	brain
27	chr4:7926600-7930600	Weak transcription	Pancreas	Pancrea
28	chr4:7926600-7930800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:7926600-7936600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:7926800-7929800	Strong transcription	Fetal Stomach	stomach
31	chr4:7926800-7930400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:7926800-7931200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:7926800-7931200	Weak transcription	Right Atrium	heart
34	chr4:7926800-7931200	Weak transcription	NHLF	lung
35	chr4:7926800-7935400	Weak transcription	Fetal Brain Male	brain
36	chr4:7927000-7930400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:7927000-7930600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:7927000-7930600	Weak transcription	Placenta	Placenta
39	chr4:7927000-7930600	Weak transcription	Hela-S3	cervix
40	chr4:7927000-7930600	Weak transcription	HSMM	muscle
41	chr4:7927000-7931000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr4:7927000-7931200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:7927000-7931200	Weak transcription	Fetal Heart	heart
44	chr4:7927200-7930600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:7927200-7930600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:7927200-7930600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:7927200-7930800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:7927400-7930400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr4:7927400-7931000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:7927600-7930600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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