Variant report

Variant	rs13139805
Chromosome Location	chr4:7917053-7917054
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs11932843	0.81[CHB][hapmap]
rs11937029	0.87[YRI][hapmap]
rs12641498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127935	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs13140004	0.81[CHB][hapmap]
rs13140108	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13151529	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1317111	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1320069	0.94[JPT][hapmap]
rs1320070	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1320071	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs1320074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1320075	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13435730	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16841396	0.83[YRI][hapmap]
rs17770147	0.81[CHB][hapmap]
rs17770447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17833038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814873	0.94[JPT][hapmap]
rs1878325	1.00[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385898	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385900	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2385901	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385902	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385908	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2385909	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2385910	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28370977	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28464089	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28489592	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28631205	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28715921	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28726254	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28734123	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28795989	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2891927	0.81[CHB][hapmap]
rs2891928	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34179701	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34317049	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34505548	0.89[AMR][1000 genomes]
rs34685551	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34701321	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34984446	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35661042	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4235268	0.94[JPT][hapmap]
rs4235269	0.93[JPT][hapmap]
rs4256209	0.81[CHB][hapmap]
rs4345163	0.94[JPT][hapmap]
rs4385040	0.93[JPT][hapmap]
rs4411970	0.81[CHB][hapmap]
rs4627847	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4689875	0.81[CHB][hapmap]
rs4696742	0.81[CHB][hapmap]
rs4696746	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696780	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4696795	0.81[ASN][1000 genomes]
rs4696827	0.93[JPT][hapmap]
rs4696834	0.94[JPT][hapmap]
rs5012708	0.94[JPT][hapmap]
rs5012709	0.93[JPT][hapmap]
rs55937650	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57831033	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446625	0.81[CHB][hapmap]
rs6811851	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6824410	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6828574	0.81[CHB][hapmap]
rs6833054	0.81[CHB][hapmap]
rs6839119	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs6839744	0.82[JPT][hapmap]
rs6844956	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs6845014	0.81[CHB][hapmap]
rs6846317	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6848540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6857814	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7437940	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7437984	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7441569	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7655918	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7663205	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7667982	0.93[JPT][hapmap]
rs7682202	0.81[CHB][hapmap]
rs7683285	0.93[JPT][hapmap]
rs7685634	0.93[JPT][hapmap]
rs7686202	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7687431	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7694650	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330348	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs938604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13139805	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:73 , 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	chr4:7909200-7925400	Weak transcription	Hela-S3	cervix
4	chr4:7911400-7917400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr4:7912000-7918000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:7912000-7931200	Weak transcription	Aorta	Aorta
7	chr4:7912600-7917200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr4:7912800-7931200	Weak transcription	Gastric	stomach
9	chr4:7913000-7927600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:7913000-7930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:7913000-7931000	Weak transcription	Fetal Intestine Large	intestine
12	chr4:7913200-7917400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:7913200-7918200	Weak transcription	Colonic Mucosa	Colon
14	chr4:7913200-7919400	Weak transcription	Right Atrium	heart
15	chr4:7913200-7919600	Weak transcription	Lung	lung
16	chr4:7913200-7926400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:7913400-7917800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:7913400-7918200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:7913400-7918800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:7913400-7919800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:7913600-7918000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr4:7913600-7926200	Weak transcription	Fetal Brain Female	brain
23	chr4:7913600-7927200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:7913600-7930400	Weak transcription	NHEK	skin
25	chr4:7913800-7919600	Weak transcription	Adipose Nuclei	Adipose
26	chr4:7913800-7925600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:7914000-7917200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:7914000-7917200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:7914000-7917800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:7914000-7917800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:7914000-7917800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:7914000-7918400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr4:7914000-7919200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:7914000-7919400	Weak transcription	Fetal Intestine Small	intestine
35	chr4:7914000-7926800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:7914200-7917200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:7914200-7917400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr4:7914200-7918200	Weak transcription	Brain Germinal Matrix	brain
39	chr4:7914200-7918800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:7914200-7919600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:7914200-7919600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:7914200-7925800	Weak transcription	HSMMtube	muscle
43	chr4:7914200-7930800	Weak transcription	Fetal Kidney	kidney
44	chr4:7914400-7918000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:7914400-7918000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr4:7914400-7925600	Weak transcription	HSMM	muscle
47	chr4:7914800-7918600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:7914800-7919200	Weak transcription	NHLF	lung
49	chr4:7914800-7919600	Weak transcription	HMEC	breast
50	chr4:7915000-7917800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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