Variant report

Variant	rs657555
Chromosome Location	chr18:12847136-12847137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12845628..12848100-chr18:12848205..12851298,3	MCF-7	breast:
2	chr18:12836682..12841337-chr18:12846526..12848726,4	MCF-7	breast:
3	chr18:12846087..12850941-chr18:12851540..12856043,5	K562	blood:
4	chr18:12845560..12847901-chr18:12888541..12891505,2	MCF-7	breast:
5	chr18:12846508..12849258-chr18:12882728..12885710,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175354	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11875687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12955302	0.85[CEU][hapmap]
rs16939895	0.93[CEU][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2847297	0.90[JPT][hapmap]
rs34846641	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs471401	0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs482160	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs484020	0.93[CEU][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs487273	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513185	0.92[YRI][hapmap]
rs514000	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs515151	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534911	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs547268	0.93[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs578377	0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs579052	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs607906	0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs612058	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622717	0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs6505765	0.85[JPT][hapmap]
rs658158	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs669822	1.00[ASW][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs7234029	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7241016	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7241650	1.00[ASW][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap]
rs8083786	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8091566	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9959425	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9966378	0.92[YRI][hapmap]

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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers 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 miRNA target site	130 gene(s)	inside rSNPs	diseases
2	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
7	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription 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	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs657555	MC5R	cis	parietal	SCAN
rs657555	CDH24	trans	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12821800-12851800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr18:12828400-12856000	Weak transcription	Fetal Kidney	kidney
3	chr18:12829000-12861200	Weak transcription	Fetal Brain Female	brain
4	chr18:12829000-12862600	Weak transcription	Brain Germinal Matrix	brain
5	chr18:12834200-12850200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr18:12838600-12848400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr18:12838600-12851800	Weak transcription	Fetal Brain Male	brain
8	chr18:12838600-12852000	Weak transcription	Ovary	ovary
9	chr18:12838600-12854000	Weak transcription	Left Ventricle	heart
10	chr18:12838600-12856000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr18:12838600-12856200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr18:12838600-12857200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr18:12838600-12861800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:12838600-12862000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr18:12838600-12862400	Weak transcription	NH-A	brain
16	chr18:12838600-12862600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr18:12838800-12851800	Weak transcription	Fetal Lung	lung
18	chr18:12838800-12852600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr18:12838800-12854600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr18:12838800-12855600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr18:12838800-12879000	Weak transcription	Psoas Muscle	Psoas
22	chr18:12839400-12861200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr18:12839600-12851600	Weak transcription	HSMMtube	muscle
24	chr18:12839600-12852000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr18:12839600-12854800	Weak transcription	Fetal Intestine Small	intestine
26	chr18:12839600-12855200	Weak transcription	Fetal Intestine Large	intestine
27	chr18:12839600-12857200	Weak transcription	Aorta	Aorta
28	chr18:12839600-12858800	Weak transcription	Adipose Nuclei	Adipose
29	chr18:12839600-12861200	Weak transcription	Brain Hippocampus Middle	brain
30	chr18:12839600-12862600	Weak transcription	HSMM	muscle
31	chr18:12839800-12853400	Weak transcription	HepG2	liver
32	chr18:12840000-12848400	Weak transcription	HMEC	breast
33	chr18:12840000-12863800	Weak transcription	Brain Anterior Caudate	brain
34	chr18:12840200-12851800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr18:12840400-12848400	Weak transcription	Liver	Liver
36	chr18:12840400-12851600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr18:12840800-12847400	Genic enhancers	Dnd41	blood
38	chr18:12840800-12849200	Weak transcription	NHEK	skin
39	chr18:12840800-12854400	Weak transcription	Hela-S3	cervix
40	chr18:12840800-12855400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr18:12840800-12858000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr18:12841000-12849200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr18:12841000-12851600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr18:12841000-12853800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr18:12841000-12855400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr18:12841000-12856000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr18:12841000-12859000	Weak transcription	Right Ventricle	heart
48	chr18:12841000-12863200	Weak transcription	Colonic Mucosa	Colon
49	chr18:12841200-12854400	Weak transcription	A549	lung
50	chr18:12841200-12855600	Weak transcription	Fetal Muscle Leg	muscle

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