Variant report

Variant	rs16954505
Chromosome Location	chr16:81074160-81074161
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81036155..81041262-chr16:81074086..81079875,7	K562	blood:
2	chr16:81073990..81076535-chr16:81110612..81112776,2	MCF-7	breast:
3	chr16:81068207..81071925-chr16:81073357..81079831,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166454	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166451	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10459871	0.89[CEU][hapmap]
rs10459872	0.89[CEU][hapmap]
rs1048194	1.00[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs10514512	0.89[CEU][hapmap]
rs10514513	0.89[CEU][hapmap]
rs10514514	0.89[CEU][hapmap]
rs10514515	0.89[CEU][hapmap]
rs11150337	0.90[EUR][1000 genomes]
rs11537	0.89[CEU][hapmap]
rs11863158	0.89[EUR][1000 genomes]
rs11865207	0.88[EUR][1000 genomes]
rs11866124	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs12443549	0.89[CEU][hapmap]
rs12444137	0.89[CEU][hapmap]
rs12444747	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12444974	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs12445303	0.89[CEU][hapmap]
rs12456	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12918103	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs12919980	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12921900	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs12922449	1.00[CHB][hapmap]
rs12927239	0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12927828	0.88[EUR][1000 genomes]
rs12928381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12928648	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12929250	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs12930202	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs12931555	0.87[ASN][1000 genomes]
rs12931678	1.00[CHB][hapmap]
rs12932466	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs13185	0.80[CEU][hapmap]
rs13333603	0.95[ASN][1000 genomes]
rs1414	0.89[CEU][hapmap]
rs1563072	0.80[CEU][hapmap]
rs1563075	0.89[CEU][hapmap]
rs16954513	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs16954572	0.89[CEU][hapmap]
rs16954582	0.89[CEU][hapmap]
rs2241408	0.97[ASN][1000 genomes]
rs2278021	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2278022	1.00[CEU][hapmap]
rs2278023	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2278024	0.86[CEU][hapmap]
rs2278025	0.87[EUR][1000 genomes]
rs2303214	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap]
rs2549891	0.88[CEU][hapmap]
rs2549893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2549896	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs2602402	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2602404	0.88[EUR][1000 genomes]
rs2602407	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs2970076	0.89[CEU][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs2970077	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes]
rs34105513	0.95[ASN][1000 genomes]
rs34545373	0.95[ASN][1000 genomes]
rs35096487	0.88[EUR][1000 genomes]
rs35552248	0.87[ASN][1000 genomes]
rs35674322	0.97[ASN][1000 genomes]
rs36040615	0.95[ASN][1000 genomes]
rs3759931	0.97[ASN][1000 genomes]
rs4324141	0.89[CEU][hapmap]
rs4889225	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs4889229	0.82[EUR][1000 genomes]
rs4889230	0.82[EUR][1000 genomes]
rs4889233	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs5023849	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs5023850	0.84[EUR][1000 genomes]
rs5023852	0.87[EUR][1000 genomes]
rs60303302	0.81[EUR][1000 genomes]
rs6420419	0.87[EUR][1000 genomes]
rs6420421	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs6564819	0.81[EUR][1000 genomes]
rs71400134	0.87[ASN][1000 genomes]
rs71400135	0.87[ASN][1000 genomes]
rs71400136	0.95[ASN][1000 genomes]
rs71400137	0.87[ASN][1000 genomes]
rs7185637	0.81[EUR][1000 genomes]
rs7200400	0.85[CHD][hapmap]
rs7203546	0.82[EUR][1000 genomes]
rs7204040	0.89[CEU][hapmap]
rs7206814	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs754429	0.89[CEU][hapmap]
rs8043855	0.89[CEU][hapmap];0.93[CHD][hapmap];0.84[EUR][1000 genomes]
rs804885	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs804895	0.80[CEU][hapmap]
rs804902	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs8052490	0.89[CEU][hapmap]
rs8056972	0.89[CEU][hapmap]
rs8059692	0.80[CEU][hapmap]
rs8177878	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs8177891	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs8177940	0.82[CEU][hapmap]
rs8177957	0.89[CEU][hapmap]
rs8177959	0.89[CEU][hapmap]
rs935942	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs9923732	0.82[CEU][hapmap]
rs9925940	0.89[CEU][hapmap]
rs9925943	0.89[CEU][hapmap]
rs9926174	0.89[CEU][hapmap]
rs9929586	0.89[CEU][hapmap]
rs9933184	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1065258	chr16:80887483-81081768	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
6	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv995083	chr16:81050917-81076406	Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1062724	chr16:81052312-81137007	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1897	chr16:81060566-81105260	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16954505	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs16954505	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs16954505	LOC100329108	cis	lymphoblastoid	seeQTL
rs16954505	GCSH	cis	lymphoblastoid	seeQTL
rs16954505	GCSH	cis	Muscle Skeletal	GTEx
rs16954505	C16orf46	Cis_1M	lymphoblastoid	RTeQTL
rs16954505	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81070600-81075800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:81070800-81081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:81071000-81074600	Enhancers	Brain Substantia Nigra	brain
4	chr16:81071000-81074600	Weak transcription	HSMM	muscle
5	chr16:81071000-81075200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr16:81071000-81075200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr16:81071000-81075400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr16:81071000-81075400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr16:81071000-81075800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr16:81071000-81076400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr16:81071000-81079800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr16:81071200-81074200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr16:81071200-81074200	Enhancers	Brain Angular Gyrus	brain
14	chr16:81071200-81074200	Enhancers	Brain Hippocampus Middle	brain
15	chr16:81071200-81074200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr16:81071200-81074400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr16:81071200-81074400	Weak transcription	Primary T cells from cord blood	blood
18	chr16:81071200-81074400	Weak transcription	Liver	Liver
19	chr16:81071200-81074400	Weak transcription	HMEC	breast
20	chr16:81071200-81074400	Weak transcription	HUVEC	blood vessel
21	chr16:81071200-81074600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr16:81071200-81074600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr16:81071200-81074600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr16:81071200-81074600	Weak transcription	A549	lung
25	chr16:81071200-81074800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr16:81071200-81075000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr16:81071200-81075000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr16:81071200-81075000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr16:81071200-81075000	Enhancers	Brain Cingulate Gyrus	brain
30	chr16:81071200-81075000	Weak transcription	Brain Germinal Matrix	brain
31	chr16:81071200-81075000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr16:81071200-81075000	Weak transcription	Fetal Kidney	kidney
33	chr16:81071200-81075000	Weak transcription	Fetal Lung	lung
34	chr16:81071200-81075000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr16:81071200-81075000	Weak transcription	Right Ventricle	heart
36	chr16:81071200-81075000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr16:81071200-81075000	Weak transcription	HSMMtube	muscle
38	chr16:81071200-81075000	Weak transcription	NHLF	lung
39	chr16:81071200-81075000	Weak transcription	Osteobl	bone
40	chr16:81071200-81075200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr16:81071200-81075200	Weak transcription	Aorta	Aorta
42	chr16:81071200-81075200	Weak transcription	Colonic Mucosa	Colon
43	chr16:81071200-81075200	Weak transcription	NHDF-Ad	bronchial
44	chr16:81071200-81075400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr16:81071200-81080400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr16:81071200-81080400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr16:81071200-81080600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr16:81071200-81082000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr16:81071200-81082400	Weak transcription	Stomach Mucosa	stomach
50	chr16:81071400-81075000	Weak transcription	Adipose Nuclei	Adipose

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