Variant report

Variant	rs4797609
Chromosome Location	chr18:12039414-12039415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:11732649..11733675-chr18:12038633..12039652,5	MCF-7	breast:
2	chr18:11655388..11656100-chr18:12038645..12039575,5	K562	blood:
3	chr18:11937505..11938532-chr18:12038635..12039615,5	MCF-7	breast:
4	chr18:11992964..11995381-chr18:12038056..12040567,2	MCF-7	breast:
5	chr18:11654951..11655937-chr18:12038618..12039570,4	MCF-7	breast:
6	chr18:11732574..11733777-chr18:12038625..12039612,8	K562	blood:

Variant related genes	Relation type
ENSG00000266955	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1662608	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1787982	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2165855	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2849394	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2849395	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2849396	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2849397	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2849398	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2849399	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2851911	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2851912	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2851913	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2851914	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2851918	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4291976	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4580259	0.96[ASN][1000 genomes]
rs4580260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4797608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4797610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4797611	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582959	0.91[ASN][1000 genomes]
rs591447	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs622443	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs627965	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs630110	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs639876	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs639966	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs640340	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs642585	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6505709	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs655651	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs657476	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8090265	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909393	chr18:12001258-12155371	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv909394	chr18:12017343-12141372	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4797609	MC5R	cis	parietal	SCAN
rs4797609	KIAA0802	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12039200-12039600	Flanking Active TSS	Hela-S3	cervix
2	chr18:12039200-12039800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:12039200-12040800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr18:12039400-12039600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr18:12039400-12039800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr18:12039400-12040200	Enhancers	HepG2	liver
7	chr18:12039400-12041000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr18:12039400-12041000	Weak transcription	HSMM	muscle
9	chr18:12039400-12041000	Weak transcription	NHDF-Ad	bronchial
10	chr18:12039400-12041000	Weak transcription	Osteobl	bone
11	chr18:12039400-12041200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr18:12039400-12041200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr18:12039400-12041200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr18:12039400-12041200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr18:12039400-12041200	Weak transcription	A549	lung
16	chr18:12039400-12041200	Weak transcription	HMEC	breast
17	chr18:12039400-12041200	Weak transcription	HSMMtube	muscle
18	chr18:12039400-12041200	Weak transcription	NH-A	brain
19	chr18:12039400-12041200	Weak transcription	NHLF	lung
20	chr18:12039400-12041400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr18:12039400-12041400	Weak transcription	NHEK	skin
22	chr18:12039400-12042600	Weak transcription	GM12878-XiMat	blood
23	chr18:12039400-12044800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr18:12039400-12045800	Weak transcription	Pancreas	Pancrea
25	chr18:12039400-12047000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr18:12039400-12047400	Weak transcription	Gastric	stomach
27	chr18:12039400-12048400	Weak transcription	Right Ventricle	heart

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