Variant report

Variant	rs13435730
Chromosome Location	chr4:7923991-7923992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7921981..7926079-chr4:7940006..7943093,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction
ENSG00000228919	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11932843	0.81[JPT][hapmap]
rs12641498	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13131154	0.81[JPT][hapmap]
rs13139805	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]
rs13140004	0.81[JPT][hapmap]
rs13140108	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13151529	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1317111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320069	1.00[JPT][hapmap]
rs1320070	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1320071	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1320074	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1320075	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17770147	0.81[JPT][hapmap]
rs17770177	0.81[JPT][hapmap]
rs17770447	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17833038	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1814873	1.00[JPT][hapmap]
rs1878325	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2385898	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385900	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2385901	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385902	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385908	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2385909	0.86[ASN][1000 genomes]
rs2385910	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28370977	0.90[ASN][1000 genomes]
rs28464089	0.87[ASN][1000 genomes]
rs28489592	0.87[ASN][1000 genomes]
rs28631205	0.85[ASN][1000 genomes]
rs28715921	0.87[ASN][1000 genomes]
rs28726254	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28734123	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2891927	0.81[JPT][hapmap]
rs2891928	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34179701	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34317049	0.90[ASN][1000 genomes]
rs34685551	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34984446	0.87[ASN][1000 genomes]
rs35661042	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4235268	1.00[JPT][hapmap]
rs4235269	1.00[JPT][hapmap]
rs4256209	0.81[JPT][hapmap]
rs4345163	1.00[JPT][hapmap]
rs4385040	1.00[JPT][hapmap]
rs4411970	0.81[JPT][hapmap]
rs4487321	0.81[JPT][hapmap]
rs4627847	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696742	0.81[JPT][hapmap]
rs4696746	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4696778	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4696779	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4696795	0.89[ASN][1000 genomes]
rs4696827	1.00[JPT][hapmap]
rs4696834	1.00[JPT][hapmap]
rs5012708	1.00[JPT][hapmap]
rs5012709	1.00[JPT][hapmap]
rs55937650	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57831033	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6811851	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6828574	0.81[JPT][hapmap]
rs6833054	0.81[JPT][hapmap]
rs6845014	0.81[JPT][hapmap]
rs6846317	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6848540	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6857814	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7437940	0.90[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7437984	0.91[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7441569	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7655918	0.84[ASN][1000 genomes]
rs7663205	0.87[ASN][1000 genomes]
rs7667982	1.00[JPT][hapmap]
rs7683285	1.00[JPT][hapmap]
rs7685634	1.00[JPT][hapmap]
rs7686202	0.90[ASN][1000 genomes]
rs7687431	0.86[ASN][1000 genomes]
rs7694650	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9330348	0.89[ASN][1000 genomes]
rs938604	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[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
rs13435730	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:63 , 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	chr4:7912000-7931200	Weak transcription	Aorta	Aorta
5	chr4:7912800-7931200	Weak transcription	Gastric	stomach
6	chr4:7913000-7927600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:7913000-7930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:7913000-7931000	Weak transcription	Fetal Intestine Large	intestine
9	chr4:7913200-7926400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:7913600-7926200	Weak transcription	Fetal Brain Female	brain
11	chr4:7913600-7927200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:7913600-7930400	Weak transcription	NHEK	skin
13	chr4:7913800-7925600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:7914000-7926800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:7914200-7925800	Weak transcription	HSMMtube	muscle
16	chr4:7914200-7930800	Weak transcription	Fetal Kidney	kidney
17	chr4:7914400-7925600	Weak transcription	HSMM	muscle
18	chr4:7915000-7926000	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:7915000-7928200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:7915000-7930400	Weak transcription	Fetal Lung	lung
21	chr4:7918800-7930400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:7919000-7925600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:7919000-7925800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:7919000-7929000	Weak transcription	Brain Germinal Matrix	brain
25	chr4:7919200-7930600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:7919400-7926200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:7919600-7925800	Weak transcription	Fetal Heart	heart
28	chr4:7919600-7930800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:7919800-7924800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:7919800-7925600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:7919800-7926200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:7919800-7930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:7919800-7931200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr4:7920000-7924200	Weak transcription	Pancreas	Pancrea
35	chr4:7920000-7925800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:7920000-7925800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:7920000-7926000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:7920000-7926400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:7920200-7925800	Weak transcription	NHLF	lung
40	chr4:7920200-7926400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:7920400-7926400	Weak transcription	Fetal Intestine Small	intestine
42	chr4:7920400-7926400	Weak transcription	Right Atrium	heart
43	chr4:7920600-7931200	Weak transcription	Lung	lung
44	chr4:7921000-7926400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr4:7921000-7930600	Weak transcription	Esophagus	oesophagus
46	chr4:7921200-7924600	Weak transcription	A549	lung
47	chr4:7921200-7925200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr4:7921200-7925400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr4:7921200-7926000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:7921200-7926000	Weak transcription	Rectal Smooth Muscle	rectum

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