Variant report

Variant	rs938604
Chromosome Location	chr4:7904363-7904364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs12641498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13127935	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs13139805	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]
rs13140108	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13151529	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1317111	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1320069	0.93[JPT][hapmap]
rs1320070	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs1320071	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs1320074	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320075	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435730	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]
rs17770447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17833038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1814873	0.93[JPT][hapmap]
rs1878325	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385898	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2385900	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2385901	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2385902	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2385908	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2385909	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2385910	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370977	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28464089	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28489592	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28622214	0.88[YRI][hapmap]
rs28631205	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28715921	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28726254	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734123	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28795989	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2891928	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34179701	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34317049	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34505548	0.87[AMR][1000 genomes]
rs34685551	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34701321	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34984446	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35661042	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4235268	0.93[JPT][hapmap]
rs4235269	0.93[JPT][hapmap]
rs4345163	0.93[JPT][hapmap]
rs4385040	0.92[JPT][hapmap]
rs4627847	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4696746	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696778	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696780	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4696827	0.93[JPT][hapmap]
rs4696834	0.93[JPT][hapmap]
rs5012708	0.93[JPT][hapmap]
rs5012709	0.92[JPT][hapmap]
rs55937650	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57831033	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6811851	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6824410	0.84[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs6839119	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs6844956	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs6846317	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6848540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857814	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7437940	0.92[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7437984	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7441569	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7655918	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7663205	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7667982	0.93[JPT][hapmap]
rs7683285	0.92[JPT][hapmap]
rs7685634	0.92[JPT][hapmap]
rs7686202	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687431	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7694650	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9330348	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs938604	AFAP1	cis	cerebellum	SCAN
rs938604	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7883200-7904400	Weak transcription	Gastric	stomach
2	chr4:7886800-7904400	Weak transcription	Small Intestine	intestine
3	chr4:7893200-7905600	Weak transcription	Brain Angular Gyrus	brain
4	chr4:7894200-7912400	Weak transcription	Fetal Intestine Large	intestine
5	chr4:7894400-7904400	Weak transcription	Left Ventricle	heart
6	chr4:7894400-7906200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:7895600-7907600	Weak transcription	Colonic Mucosa	Colon
8	chr4:7896800-7904400	Weak transcription	Adipose Nuclei	Adipose
9	chr4:7896800-7904400	Weak transcription	Spleen	Spleen
10	chr4:7896800-7907600	Weak transcription	Fetal Intestine Small	intestine
11	chr4:7897000-7907400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:7897400-7905800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:7898600-7904400	Enhancers	A549	lung
14	chr4:7898800-7905200	Enhancers	Colon Smooth Muscle	Colon
15	chr4:7899200-7905800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:7899600-7907000	Enhancers	Fetal Brain Male	brain
17	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:7900000-7905000	Weak transcription	HMEC	breast
19	chr4:7900000-7906400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:7900000-7907400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:7900200-7905400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:7900200-7905600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr4:7900200-7912400	Weak transcription	NHEK	skin
24	chr4:7900400-7904400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr4:7900400-7904600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr4:7900400-7905800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:7900800-7905000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr4:7900800-7906000	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr4:7900800-7914400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr4:7901000-7904400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr4:7901000-7904400	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr4:7901000-7905200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr4:7901000-7905600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:7901000-7905800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:7901000-7907400	Enhancers	HSMMtube	muscle
36	chr4:7901000-7909000	Enhancers	Fetal Brain Female	brain
37	chr4:7901200-7905200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:7901400-7909400	Enhancers	Fetal Lung	lung
39	chr4:7901600-7905000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:7901600-7905800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:7901600-7907400	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr4:7901600-7914400	Enhancers	Fetal Muscle Leg	muscle
43	chr4:7901800-7905400	Genic enhancers	Osteobl	bone
44	chr4:7901800-7905800	Enhancers	Muscle Satellite Cultured Cells	--
45	chr4:7901800-7905800	Enhancers	HUVEC	blood vessel
46	chr4:7902000-7904600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:7902000-7905000	Genic enhancers	NH-A	brain
48	chr4:7902000-7909200	Enhancers	Fetal Heart	heart
49	chr4:7902000-7909400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:7902200-7905600	Enhancers	NHDF-Ad	bronchial

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