Variant report

Variant	rs16976887
Chromosome Location	chr18:11986656-11986657
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:11981504..11983527-chr18:11985199..11986981,3	MCF-7	breast:
2	chr18:11979366..11983605-chr18:11984399..11987435,4	MCF-7	breast:
3	chr18:11978886..11981038-chr18:11986460..11988368,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141401	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11660567	0.85[CHB][hapmap]
rs28475846	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28499558	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28509217	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28548932	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239304	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56364728	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57967783	0.98[ASN][1000 genomes]
rs58556096	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59796048	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59889312	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604420	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs61383190	0.90[ASN][1000 genomes]
rs6505700	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505701	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653073	0.85[ASN][1000 genomes]
rs653074	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs663591	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs67450563	0.85[ASN][1000 genomes]
rs67932171	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7230346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7240032	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7244678	0.95[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs72871698	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72871700	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72871702	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72873509	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72873510	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72873549	0.88[ASN][1000 genomes]
rs7407928	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7407929	0.84[EUR][1000 genomes]
rs7506045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8095694	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs9973177	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16976887	C13orf18	trans	lymphoblastoid	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982400-11987600	Weak transcription	Fetal Heart	heart
2	chr18:11982400-11988400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr18:11982400-12005000	Weak transcription	Aorta	Aorta
4	chr18:11982600-11986800	Weak transcription	Brain Germinal Matrix	brain
5	chr18:11982600-11987400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr18:11982600-11987800	Weak transcription	NHLF	lung
7	chr18:11982600-11995600	Weak transcription	Primary T cells from cord blood	blood
8	chr18:11982600-11995800	Weak transcription	Thymus	Thymus
9	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
10	chr18:11983400-11987400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr18:11983400-11989000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr18:11983400-11989200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr18:11983400-11989600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:11983400-11994000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr18:11983600-11989400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr18:11984000-11986800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr18:11984000-11989000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr18:11984200-11987000	Weak transcription	Adipose Nuclei	Adipose
19	chr18:11984200-11987400	Weak transcription	Fetal Lung	lung
20	chr18:11984200-11988200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr18:11984200-11988400	Weak transcription	Fetal Intestine Large	intestine
22	chr18:11984200-11989800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr18:11984200-11993600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr18:11984200-11994600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr18:11984400-11986800	Weak transcription	A549	lung
26	chr18:11984400-11987000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr18:11984400-11987000	Weak transcription	Fetal Muscle Leg	muscle
28	chr18:11984400-11987600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr18:11984400-11988400	Weak transcription	Esophagus	oesophagus
30	chr18:11984400-11988800	Weak transcription	Colonic Mucosa	Colon
31	chr18:11984400-11989200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr18:11984400-11989200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr18:11984400-11989400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr18:11984400-11989600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr18:11984400-11990000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr18:11984400-11990400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr18:11984400-11993400	Weak transcription	Lung	lung
38	chr18:11984400-11994200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr18:11984400-11994200	Weak transcription	NHEK	skin
40	chr18:11984400-11995000	Weak transcription	GM12878-XiMat	blood
41	chr18:11984600-11988400	Weak transcription	HSMMtube	muscle
42	chr18:11984600-11988600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr18:11984600-11989800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr18:11985200-11991200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr18:11985400-11987000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr18:11985400-11987200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr18:11985600-11986800	Enhancers	HepG2	liver
48	chr18:11985600-11987000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
49	chr18:11985600-11987000	Genic enhancers	Pancreas	Pancrea
50	chr18:11985600-11987200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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