Variant report

Variant	rs2278024
Chromosome Location	chr16:81079233-81079234
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:81071649..81074411-chr16:81077568..81081037,5	K562	blood:
2	chr16:81036155..81041262-chr16:81074086..81079875,7	K562	blood:
3	chr16:81079124..81081324-chr16:81108585..81111174,2	K562	blood:
4	chr16:81068207..81071925-chr16:81073357..81079831,13	MCF-7	breast:
5	chr16:81078751..81080848-chr16:81181095..81182686,2	K562	blood:
6	chr16:81078691..81081572-chr16:81082090..81085180,4	K562	blood:
7	chr16:81074762..81077123-chr16:81078708..81080321,2	K562	blood:
8	chr16:81076434..81078165-chr16:81078716..81082306,3	MCF-7	breast:
9	chr16:81069446..81072291-chr16:81077678..81081761,3	K562	blood:
10	chr16:81075103..81077247-chr16:81078361..81079890,2	MCF-7	breast:
11	chr16:81068994..81072999-chr16:81079171..81083841,7	MCF-7	breast:
12	chr16:81072851..81076497-chr16:81077627..81082197,6	K562	blood:

No data

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

Extended variants
information (count: 118 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1035541	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10459871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10459872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1048194	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs1050364	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514512	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10514513	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10514514	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514515	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11150337	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11150338	0.88[ASN][1000 genomes]
rs11537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11863158	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11865207	0.85[EUR][1000 genomes]
rs11866124	0.88[CEU][hapmap]
rs12443549	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12444137	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12444747	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs12444969	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12444974	0.88[CEU][hapmap]
rs12445303	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12456	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs12598621	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12927239	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs12927828	0.85[EUR][1000 genomes]
rs13185	0.88[CEU][hapmap]
rs1410	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1412	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1414	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1563072	0.88[CEU][hapmap]
rs1563075	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1563077	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16954505	0.86[CEU][hapmap]
rs16954513	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs16954572	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16954582	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2278022	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278025	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2287995	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2316730	1.00[CEU][hapmap]
rs2316731	1.00[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs2317085	0.84[EUR][1000 genomes]
rs2317086	0.82[EUR][1000 genomes]
rs2549891	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2549896	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2602402	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2602404	0.85[EUR][1000 genomes]
rs2602407	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs28391685	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28613188	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28672349	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2970076	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2970077	0.86[CEU][hapmap]
rs35096487	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4306521	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4324141	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4324142	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4324143	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4454990	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs4889225	1.00[CEU][hapmap]
rs4889227	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4889231	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4889233	0.88[CEU][hapmap]
rs55939311	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56032321	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56119129	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56166222	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56198248	0.81[EUR][1000 genomes]
rs56395947	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58144189	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59177227	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59685942	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61082942	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62054594	0.93[ASN][1000 genomes]
rs6420421	0.88[CEU][hapmap]
rs7188508	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7204040	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7206814	1.00[CEU][hapmap]
rs754429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8043855	1.00[CEU][hapmap]
rs804885	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs804889	0.93[CHB][hapmap];0.86[ASN][1000 genomes]
rs804895	0.88[CEU][hapmap];0.93[CHB][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs804897	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs804902	1.00[CEU][hapmap]
rs8052490	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8056972	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8059692	0.88[CEU][hapmap]
rs8177939	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8177940	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8177942	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8177943	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8177945	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8177948	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8177950	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8177957	1.00[CEU][hapmap]
rs8177959	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs889516	0.83[AMR][1000 genomes]
rs935942	1.00[CEU][hapmap]
rs9806918	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923732	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9925940	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9925943	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9926174	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9929586	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9933184	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9938965	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
10	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
11	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2278024	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs2278024	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs2278024	C16orf46	Cis_1M	lymphoblastoid	RTeQTL
rs2278024	GCSH	cis	Muscle Skeletal	GTEx
rs2278024	ATMIN	cis	Muscle Skeletal	GTEx
rs2278024	GCSH///LOC654085///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	chr16:81070800-81081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:81071000-81079800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr16:81071200-81080400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr16:81071200-81080400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr16:81071200-81080600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr16:81071200-81082000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:81071200-81082400	Weak transcription	Stomach Mucosa	stomach
8	chr16:81071400-81079400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr16:81071400-81079600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr16:81071400-81079800	Strong transcription	Fetal Intestine Large	intestine
11	chr16:81071600-81080600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:81071800-81081800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr16:81072000-81079400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr16:81072200-81079400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr16:81072400-81079800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr16:81073000-81079800	Strong transcription	Fetal Muscle Leg	muscle
17	chr16:81073600-81079800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr16:81073800-81079400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr16:81073800-81079800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr16:81073800-81079800	Strong transcription	Fetal Thymus	thymus
21	chr16:81073800-81079800	Strong transcription	Dnd41	blood
22	chr16:81074000-81079400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr16:81074000-81079400	Strong transcription	Lung	lung
24	chr16:81074000-81079400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr16:81074000-81079800	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr16:81074000-81079800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr16:81074000-81080000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr16:81074000-81080400	Strong transcription	Primary B cells from cord blood	blood
29	chr16:81074000-81080400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr16:81074000-81082400	Weak transcription	Fetal Heart	heart
31	chr16:81074200-81079400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr16:81074200-81079800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr16:81074400-81079400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr16:81074400-81079400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr16:81074400-81079400	Strong transcription	HMEC	breast
36	chr16:81074400-81079400	Strong transcription	HUVEC	blood vessel
37	chr16:81074400-81079800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr16:81074400-81079800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr16:81074400-81079800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr16:81074400-81079800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:81074400-81079800	Strong transcription	Liver	Liver
42	chr16:81074400-81079800	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr16:81074400-81080000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr16:81074400-81080200	Strong transcription	Primary T cells from cord blood	blood
45	chr16:81074600-81079400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr16:81074600-81079400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr16:81074600-81079600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr16:81074600-81079600	Strong transcription	HSMM	muscle
49	chr16:81074600-81079800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr16:81074600-81080000	Strong transcription	A549	lung

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