Variant report

Variant	rs12543038
Chromosome Location	chr8:104244309-104244310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:104224914..104226448-chr8:104241581..104244349,2	MCF-7	breast:
2	chr8:104242810..104245479-chr8:104246460..104249581,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164929	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1138873	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12541167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12543973	0.83[TSI][hapmap]
rs13275377	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13278361	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13278540	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13279226	0.87[ASN][1000 genomes]
rs1353212	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1353213	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1403293	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1494278	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1522707	0.82[GIH][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes]
rs1568641	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16870243	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16870245	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16870249	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17205332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17799604	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1982892	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1982893	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2131860	0.82[MEX][hapmap]
rs2220825	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2270525	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs3104029	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3104031	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3104033	0.81[JPT][hapmap]
rs3107646	0.85[GIH][hapmap];0.94[MEX][hapmap];0.89[AMR][1000 genomes]
rs3107648	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs3107649	0.80[AMR][1000 genomes]
rs3116457	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3116462	0.88[AMR][1000 genomes]
rs3116464	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3116466	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3116468	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs3133820	0.87[AMR][1000 genomes]
rs3133821	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3133824	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3133825	0.88[CEU][hapmap];0.80[AMR][1000 genomes]
rs3133833	0.81[JPT][hapmap]
rs3133835	1.00[ASW][hapmap]
rs3133836	1.00[ASW][hapmap]
rs3133837	0.81[JPT][hapmap]
rs34185273	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34201011	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34273148	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34337822	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4734693	0.90[ASN][1000 genomes]
rs4734695	0.90[ASN][1000 genomes]
rs7002269	0.94[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9656787	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831413	chr8:104085141-104269789	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	esv14660	chr8:104182119-104245529	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1015965	chr8:104192086-104361108	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv1017326	chr8:104236193-104313235	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12543038	FZD6	cis	cerebellum	SCAN
rs12543038	BAALC	cis	parietal	SCAN
rs12543038	SLC25A32	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104227600-104245400	Weak transcription	Fetal Brain Male	brain
2	chr8:104238400-104245200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:104242000-104245200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr8:104242400-104251200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr8:104242400-104251200	Weak transcription	HMEC	breast
6	chr8:104242600-104245600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr8:104242800-104245400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr8:104242800-104250200	Weak transcription	Fetal Brain Female	brain
9	chr8:104243200-104248600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr8:104243600-104244600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr8:104243800-104244400	Weak transcription	Brain Angular Gyrus	brain
12	chr8:104243800-104244400	Weak transcription	Brain Anterior Caudate	brain
13	chr8:104243800-104244600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr8:104243800-104246400	Weak transcription	Psoas Muscle	Psoas
15	chr8:104243800-104248000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr8:104243800-104248000	Weak transcription	Osteobl	bone
17	chr8:104243800-104248200	Weak transcription	NHLF	lung
18	chr8:104244000-104244800	Weak transcription	Aorta	Aorta
19	chr8:104244000-104245200	Strong transcription	Primary hematopoietic stem cells	blood
20	chr8:104244000-104251200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr8:104244000-104268400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr8:104244200-104245600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr8:104244200-104248000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr8:104244200-104251400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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