Variant report

Variant	rs394408
Chromosome Location	chr4:74849352-74849353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr4:74849214-74849423	HepG2	liver:	n/a	n/a
2	MAFK	chr4:74849270-74849455	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:74849171..74851572-chr4:74855795..74857358,2	K562	blood:

Variant related genes	Relation type
PF4	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1025596	0.81[EUR][1000 genomes]
rs1156553	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1156554	1.00[CEU][hapmap]
rs13117734	0.83[EUR][1000 genomes]
rs1594229	0.83[EUR][1000 genomes]
rs1594230	0.83[EUR][1000 genomes]
rs164615	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs164617	0.83[EUR][1000 genomes]
rs168449	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168450	0.83[EUR][1000 genomes]
rs16850352	1.00[JPT][hapmap]
rs16850354	1.00[JPT][hapmap]
rs1821623	0.83[EUR][1000 genomes]
rs183028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1836663	0.83[EUR][1000 genomes]
rs187080	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs187082	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs189511	0.83[EUR][1000 genomes]
rs1898002	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs191601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2043537	0.83[EUR][1000 genomes]
rs2117721	0.83[EUR][1000 genomes]
rs240610	0.83[EUR][1000 genomes]
rs2437285	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2457996	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2472655	0.83[EUR][1000 genomes]
rs2564594	0.89[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs351997	0.83[EUR][1000 genomes]
rs352007	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352010	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs352013	0.83[EUR][1000 genomes]
rs352018	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs352023	0.83[EUR][1000 genomes]
rs352024	0.83[EUR][1000 genomes]
rs352026	0.83[EUR][1000 genomes]
rs352027	0.83[EUR][1000 genomes]
rs352045	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs352046	0.86[EUR][1000 genomes]
rs352047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs3756075	1.00[JPT][hapmap]
rs377579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409336	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs416046	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs420389	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs425535	0.83[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs426901	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs434988	0.83[EUR][1000 genomes]
rs440676	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs442155	0.91[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes]
rs447206	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs450373	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4694656	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs487834	0.83[EUR][1000 genomes]
rs552582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs599746	0.83[EUR][1000 genomes]
rs614822	0.83[EUR][1000 genomes]
rs6820253	0.83[EUR][1000 genomes]
rs6838264	1.00[JPT][hapmap]

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	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1006029	chr4:74793922-74986664	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs394408	CXCL5	cis	multi-tissue	Pritchard
rs394408	NAAA	cis	cerebellum	SCAN
rs394408	MOBKL1A	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74837000-74850800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:74845200-74850600	Weak transcription	NHDF-Ad	bronchial
3	chr4:74845400-74853400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:74845600-74853000	Weak transcription	K562	blood
5	chr4:74846200-74849400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:74847600-74849400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:74847600-74850000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:74847800-74850000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:74847800-74852000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr4:74848200-74850000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:74848200-74852800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr4:74848200-74853600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:74848400-74850000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:74848400-74853400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:74848600-74850000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:74848600-74852000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr4:74848600-74853600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:74848600-74863000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:74848800-74849800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:74848800-74850000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:74848800-74850200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:74848800-74850200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:74849000-74849600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:74849200-74850600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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