Variant report

Variant	rs6554996
Chromosome Location	chr5:17356166-17356167
allele	A/C
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	STAT3	chr5:17356060-17356389	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr5:17356019-17356576	MCF10A-Er-Src	breast:	n/a	n/a
3	SETDB1	chr5:17356025-17356756	U2OS	brain:	n/a	n/a
4	FOS	chr5:17356020-17356443	MCF10A-Er-Src	breast:	n/a	chr5:17356250-17356261 chr5:17356172-17356183
5	CEBPB	chr5:17356136-17356434	IMR90	lung:	n/a	n/a
6	FOS	chr5:17356012-17356441	MCF10A-Er-Src	breast:	n/a	chr5:17356250-17356261 chr5:17356172-17356183
7	STAT3	chr5:17356132-17356355	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr5:17356078-17356392	HUVEC	blood vessel:	n/a	chr5:17356250-17356261 chr5:17356172-17356183
9	FOS	chr5:17356011-17356504	MCF10A-Er-Src	breast:	n/a	chr5:17356250-17356261 chr5:17356172-17356183
10	FOS	chr5:17356035-17356437	MCF10A-Er-Src	breast:	n/a	chr5:17356250-17356261 chr5:17356172-17356183
11	MYC	chr5:17356129-17356390	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
FTH1P10	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs13178605	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500506	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1500507	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1972037	0.81[CEU][hapmap];0.90[ASN][1000 genomes]
rs2008011	0.80[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs2055875	0.85[ASN][1000 genomes]
rs298552	0.85[EUR][1000 genomes]
rs298553	0.86[EUR][1000 genomes]
rs34875290	0.89[ASN][1000 genomes]
rs35497365	0.90[ASN][1000 genomes]
rs4382171	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4701683	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4701684	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4701685	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4702207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4702208	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554994	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554995	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554998	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6861179	0.88[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6876143	0.80[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6887129	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704602	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7704923	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7705370	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs7705848	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7706156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7715898	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7727410	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7730990	0.87[ASN][1000 genomes]
rs7733712	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs867356	0.89[ASN][1000 genomes]
rs964751	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs964752	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv461988	chr5:17296342-17484038	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv597313	chr5:17296342-17484038	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv830219	chr5:17325802-17518914	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv2763872	chr5:17342482-17358269	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
6	esv3432739	chr5:17342737-17357177	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
7	esv19164	chr5:17342748-17357008	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
8	esv1836524	chr5:17347702-17356239	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
9	nsv441940	chr5:17347702-17356239	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
10	nsv597318	chr5:17347706-17356166	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
11	nsv597319	chr5:17347706-17356536	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
12	nsv597320	chr5:17347706-17356614	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
13	nsv597323	chr5:17351275-17356166	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
14	nsv597324	chr5:17352210-17356614	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
15	nsv597325	chr5:17352326-17356166	Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
16	nsv597326	chr5:17352326-17356614	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
17	nsv597327	chr5:17352407-17356166	Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
18	nsv597328	chr5:17352407-17356614	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
19	nsv597329	chr5:17352741-17356614	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
20	nsv968879	chr5:17353620-17359144	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6554996	GPR75	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17344600-17358400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:17354800-17366000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:17355600-17356400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:17355800-17356600	Enhancers	Muscle Satellite Cultured Cells	--
5	chr5:17355800-17356600	Enhancers	NHDF-Ad	bronchial
6	chr5:17356000-17356200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:17356000-17356400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:17356000-17356800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
9	chr5:17356000-17359400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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