Variant report

Variant	rs484020
Chromosome Location	chr18:12855440-12855441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12854011..12857455-chr18:12881831..12884967,4	K562	blood:
2	chr18:12853108..12856938-chr18:12881007..12885232,4	MCF-7	breast:
3	chr18:12846087..12850941-chr18:12851540..12856043,5	K562	blood:
4	chr18:12854850..12856637-chr18:12934823..12937268,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175354	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11875687	0.93[CEU][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16939895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847297	0.85[JPT][hapmap]
rs34846641	0.86[EUR][1000 genomes]
rs482160	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487273	0.92[CEU][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs514000	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515151	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs534911	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs579052	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs612058	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs657555	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]
rs658158	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7234029	0.85[CEU][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs7241016	0.85[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs8083786	0.88[EUR][1000 genomes]
rs8091305	0.84[MKK][hapmap]
rs8091566	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9959061	0.87[MKK][hapmap]
rs9959425	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	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	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
3	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
4	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
5	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
rs484020	CDH24	trans	parietal	SCAN
rs484020	C18orf1	cis	lymphoblastoid	seeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12828400-12856000	Weak transcription	Fetal Kidney	kidney
2	chr18:12829000-12861200	Weak transcription	Fetal Brain Female	brain
3	chr18:12829000-12862600	Weak transcription	Brain Germinal Matrix	brain
4	chr18:12838600-12856000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr18:12838600-12856200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr18:12838600-12857200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr18:12838600-12861800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr18:12838600-12862000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr18:12838600-12862400	Weak transcription	NH-A	brain
10	chr18:12838600-12862600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr18:12838800-12855600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr18:12838800-12879000	Weak transcription	Psoas Muscle	Psoas
13	chr18:12839400-12861200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr18:12839600-12857200	Weak transcription	Aorta	Aorta
15	chr18:12839600-12858800	Weak transcription	Adipose Nuclei	Adipose
16	chr18:12839600-12861200	Weak transcription	Brain Hippocampus Middle	brain
17	chr18:12839600-12862600	Weak transcription	HSMM	muscle
18	chr18:12840000-12863800	Weak transcription	Brain Anterior Caudate	brain
19	chr18:12840800-12858000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr18:12841000-12856000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr18:12841000-12859000	Weak transcription	Right Ventricle	heart
22	chr18:12841000-12863200	Weak transcription	Colonic Mucosa	Colon
23	chr18:12841200-12855600	Weak transcription	Fetal Muscle Leg	muscle
24	chr18:12841400-12856200	Weak transcription	Pancreas	Pancrea
25	chr18:12841400-12863400	Weak transcription	Esophagus	oesophagus
26	chr18:12843400-12857200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr18:12843600-12856000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr18:12843600-12861400	Weak transcription	Fetal Heart	heart
29	chr18:12843800-12856000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr18:12843800-12856200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr18:12843800-12856200	Weak transcription	Gastric	stomach
32	chr18:12844000-12855800	Weak transcription	Lung	lung
33	chr18:12844000-12856000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr18:12844200-12879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr18:12844400-12856200	Weak transcription	Spleen	Spleen
36	chr18:12844400-12862600	Weak transcription	K562	blood
37	chr18:12844600-12855600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr18:12844600-12856000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr18:12844600-12862400	Weak transcription	Small Intestine	intestine
40	chr18:12845400-12855600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr18:12846200-12857200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr18:12846200-12857200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr18:12846800-12857200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr18:12846800-12857200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr18:12847200-12862600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr18:12848800-12858600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr18:12849000-12862600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr18:12849200-12861200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr18:12849200-12861200	Weak transcription	HMEC	breast
50	chr18:12849400-12856000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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