Variant report

Variant	rs12456
Chromosome Location	chr16:81065059-81065060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:81065029-81065291	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr16:81064912-81065374	K562	blood:	n/a	n/a
3	POLR2A	chr16:81064876-81065108	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:81064714-81066411	K562	blood:	n/a	n/a
5	POLR2A	chr16:81065058-81065396	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:81061882..81066764-chr16:81067446..81071538,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATMIN-1	chr16:81064375-81065090	ENSG00000261061.1

Variant related genes	Relation type
ATMIN	TF binding region
ENSG00000260213	Chromatin interaction
ENSG00000166454	Chromatin interaction

Extended variants
information (count: 146 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1035541	0.86[EUR][1000 genomes]
rs10459871	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs10459872	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs10468366	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1048194	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.98[EUR][1000 genomes]
rs1050364	0.82[EUR][1000 genomes]
rs10514512	0.89[CEU][hapmap]
rs10514513	0.89[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs10514514	0.89[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs10514515	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11537	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs11866124	0.80[CEU][hapmap];1.00[MEX][hapmap]
rs12443549	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs12444137	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs12444747	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12444969	0.83[EUR][1000 genomes]
rs12444974	0.80[CEU][hapmap];1.00[MEX][hapmap]
rs12445303	0.89[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs12448806	0.83[EUR][1000 genomes]
rs12598621	0.82[EUR][1000 genomes]
rs12927239	0.88[TSI][hapmap]
rs13185	0.80[CEU][hapmap]
rs13332530	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1412	0.81[EUR][1000 genomes]
rs1414	0.89[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1563072	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs1563075	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs1563077	0.82[EUR][1000 genomes]
rs16954505	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs16954513	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs16954525	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[ASN][1000 genomes]
rs16954528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs16954572	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs16954582	0.89[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1869347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2278022	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2278024	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs2287995	0.85[EUR][1000 genomes]
rs2316730	1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs2317087	0.83[EUR][1000 genomes]
rs2549891	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2549896	0.89[CEU][hapmap]
rs2602402	0.89[CEU][hapmap]
rs2602407	0.89[CEU][hapmap]
rs28391685	0.82[EUR][1000 genomes]
rs28613188	0.82[EUR][1000 genomes]
rs28672349	0.82[EUR][1000 genomes]
rs2970076	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs2970077	1.00[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs4306521	0.82[EUR][1000 genomes]
rs4324141	0.89[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs4324142	0.82[EUR][1000 genomes]
rs4324143	0.82[EUR][1000 genomes]
rs4889225	0.89[CEU][hapmap]
rs4889227	0.82[EUR][1000 genomes]
rs4889231	0.82[EUR][1000 genomes]
rs4889233	0.80[CEU][hapmap]
rs55664147	0.92[ASN][1000 genomes]
rs55939311	0.80[EUR][1000 genomes]
rs56032321	0.82[EUR][1000 genomes]
rs56119129	0.82[EUR][1000 genomes]
rs56166222	0.80[EUR][1000 genomes]
rs56198248	0.87[EUR][1000 genomes]
rs56286107	0.86[EUR][1000 genomes]
rs56333013	0.92[ASN][1000 genomes]
rs56395947	0.82[EUR][1000 genomes]
rs56758545	0.92[ASN][1000 genomes]
rs56838270	0.92[ASN][1000 genomes]
rs57435835	0.84[ASN][1000 genomes]
rs57830624	0.92[ASN][1000 genomes]
rs58144189	0.88[EUR][1000 genomes]
rs59177227	0.82[EUR][1000 genomes]
rs59685942	0.82[EUR][1000 genomes]
rs6420421	0.80[CEU][hapmap]
rs6564815	0.92[ASN][1000 genomes]
rs6564816	0.92[ASN][1000 genomes]
rs7187063	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7188508	0.82[EUR][1000 genomes]
rs7198494	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7204040	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7206814	0.89[CEU][hapmap]
rs73597252	0.84[EUR][1000 genomes]
rs74028898	0.92[ASN][1000 genomes]
rs74028901	0.92[ASN][1000 genomes]
rs74028902	0.84[ASN][1000 genomes]
rs74030503	0.84[ASN][1000 genomes]
rs754429	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs8043855	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs8045625	1.00[CHB][hapmap]
rs804885	0.89[CEU][hapmap]
rs804895	0.80[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs804897	0.87[EUR][1000 genomes]
rs804902	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs8052490	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs8056972	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs8059692	0.80[CEU][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs8061024	1.00[JPT][hapmap]
rs8177851	0.81[EUR][1000 genomes]
rs8177857	1.00[JPT][hapmap]
rs8177858	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8177859	1.00[JPT][hapmap]
rs8177868	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8177871	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8177872	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8177874	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8177876	0.84[EUR][1000 genomes]
rs8177877	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8177879	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8177890	1.00[JPT][hapmap]
rs8177895	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8177905	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8177917	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs8177940	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs8177941	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8177942	0.80[EUR][1000 genomes]
rs8177943	0.82[EUR][1000 genomes]
rs8177945	0.80[EUR][1000 genomes]
rs8177948	0.82[EUR][1000 genomes]
rs8177950	0.82[EUR][1000 genomes]
rs8177957	0.89[CEU][hapmap]
rs8177959	0.89[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs874437	0.84[EUR][1000 genomes]
rs935942	0.89[CEU][hapmap]
rs9806918	0.83[EUR][1000 genomes]
rs9923732	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs9925940	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs9925943	0.89[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9926174	0.89[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9929586	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs9933184	0.89[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9934220	1.00[JPT][hapmap]
rs9938965	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	esv1802804	chr16:81061827-81070110	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	esv1838483	chr16:81061827-81070110	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	esv1841728	chr16:81061827-81070110	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12456	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs12456	BM039	cis	multi-tissue	Pritchard
rs12456	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs12456	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs12456	ATMIN	cis	Muscle Skeletal	GTEx
rs12456	DC13	cis	multi-tissue	Pritchard
rs12456	GCSH	trans	brain	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81041800-81069000	Weak transcription	Ovary	ovary
2	chr16:81041800-81069000	Weak transcription	Small Intestine	intestine
3	chr16:81042000-81069000	Weak transcription	Esophagus	oesophagus
4	chr16:81042000-81069000	Weak transcription	Pancreas	Pancrea
5	chr16:81042000-81069600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr16:81042200-81068800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr16:81042200-81069000	Weak transcription	Colonic Mucosa	Colon
8	chr16:81042200-81069600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr16:81042400-81069000	Weak transcription	Brain Germinal Matrix	brain
10	chr16:81042400-81069000	Weak transcription	Fetal Heart	heart
11	chr16:81043000-81065400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr16:81043200-81065200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr16:81044000-81065200	Strong transcription	Thymus	Thymus
14	chr16:81044800-81065200	Strong transcription	Hela-S3	cervix
15	chr16:81045200-81065200	Strong transcription	A549	lung
16	chr16:81045400-81065200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr16:81047800-81069000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr16:81048400-81069000	Weak transcription	Fetal Kidney	kidney
19	chr16:81048600-81069000	Weak transcription	Fetal Brain Female	brain
20	chr16:81049000-81069000	Weak transcription	Right Ventricle	heart
21	chr16:81050200-81069000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr16:81050600-81069000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr16:81053000-81069400	Weak transcription	Aorta	Aorta
24	chr16:81053400-81068800	Weak transcription	Brain Angular Gyrus	brain
25	chr16:81053600-81069000	Weak transcription	Brain Anterior Caudate	brain
26	chr16:81053800-81068800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr16:81054000-81068800	Weak transcription	Brain Substantia Nigra	brain
28	chr16:81054200-81069000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr16:81055200-81068800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr16:81055200-81069400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr16:81055200-81069600	Weak transcription	Spleen	Spleen
32	chr16:81055400-81069000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr16:81055400-81069200	Weak transcription	NHLF	lung
34	chr16:81055600-81069000	Weak transcription	Lung	lung
35	chr16:81055600-81069400	Weak transcription	Gastric	stomach
36	chr16:81055600-81069600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr16:81055800-81069000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr16:81055800-81069400	Weak transcription	Left Ventricle	heart
39	chr16:81055800-81069600	Weak transcription	HSMMtube	muscle
40	chr16:81056200-81069600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr16:81056600-81068800	Weak transcription	Brain Hippocampus Middle	brain
42	chr16:81057000-81069000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr16:81057000-81069000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr16:81057000-81069600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr16:81057200-81069000	Weak transcription	Primary B cells from cord blood	blood
46	chr16:81057600-81069400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr16:81057800-81069400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:81058200-81069000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr16:81060400-81065400	Strong transcription	Fetal Stomach	stomach
50	chr16:81060600-81065200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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