Variant report

Variant	rs935942
Chromosome Location	chr16:81112136-81112137
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:81112056-81112205	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr16:81110156-81112906	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:81073990..81076535-chr16:81110612..81112776,2	MCF-7	breast:
2	chr16:81109459..81113813-chr16:81119137..81125158,9	MCF-7	breast:
3	chr16:81067728..81071580-chr16:81109086..81113987,13	K562	blood:
4	chr16:81109242..81112738-chr16:81125910..81131139,12	MCF-7	breast:
5	chr16:81096522..81104265-chr16:81107324..81112531,10	MCF-7	breast:
6	chr16:81102378..81105736-chr16:81109275..81112562,6	K562	blood:
7	chr16:81038376..81043277-chr16:81108432..81112403,6	K562	blood:
8	chr16:81110316..81112473-chr16:81346981..81348533,2	MCF-7	breast:
9	chr16:81110779..81112641-chr16:81230562..81234042,3	MCF-7	breast:
10	chr16:81109389..81113385-chr16:81129533..81131576,3	K562	blood:
11	chr16:81108969..81114076-chr16:81128464..81132360,7	K562	blood:
12	chr16:81067084..81072191-chr16:81106033..81112629,21	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATMIN-4	chr16:81111937-81112455	ENSG00000245059
2	lnc-ATMIN-4	chr16:81111937-81112466	ENSG00000245059.2

No data

Variant related genes	Relation type
C16orf46	TF binding region
ENSG00000166454	Chromatin interaction
ENSG00000140905	Chromatin interaction
ENSG00000166473	Chromatin interaction
ENSG00000261838	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000260643	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000260495	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1035541	0.82[EUR][1000 genomes]
rs10459871	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs10459872	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs1048194	0.89[CEU][hapmap]
rs1050364	0.89[EUR][1000 genomes]
rs10514512	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10514513	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs10514514	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs10514515	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11150337	0.89[EUR][1000 genomes]
rs11537	1.00[CEU][hapmap];0.87[MEX][hapmap]
rs11863158	0.88[EUR][1000 genomes]
rs11865207	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11866124	0.90[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs12443549	1.00[CEU][hapmap];0.88[MEX][hapmap];0.87[EUR][1000 genomes]
rs12444137	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12444747	0.89[CEU][hapmap]
rs12444974	0.90[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs12445303	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs12456	0.89[CEU][hapmap]
rs12598621	0.89[EUR][1000 genomes]
rs12927239	0.89[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12927828	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13185	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs1410	0.85[EUR][1000 genomes]
rs1412	0.87[EUR][1000 genomes]
rs1414	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs1563072	0.90[CEU][hapmap]
rs1563075	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1563077	0.89[EUR][1000 genomes]
rs16954505	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs16954513	0.89[CEU][hapmap]
rs16954572	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs16954582	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs2257378	0.81[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs2278022	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs2278024	1.00[CEU][hapmap]
rs2278025	0.83[EUR][1000 genomes]
rs2316730	0.89[CEU][hapmap]
rs2316731	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2317085	0.83[EUR][1000 genomes]
rs2317086	0.82[EUR][1000 genomes]
rs2549891	1.00[CEU][hapmap];0.94[MEX][hapmap]
rs2549895	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2549896	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2549899	0.81[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap]
rs2602401	0.88[CHD][hapmap]
rs2602402	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2602404	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2602407	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602431	0.86[CHD][hapmap];0.88[MEX][hapmap]
rs28391685	0.89[EUR][1000 genomes]
rs28613188	0.89[EUR][1000 genomes]
rs28672349	0.89[EUR][1000 genomes]
rs2970076	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2970077	0.89[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs35096487	0.87[EUR][1000 genomes]
rs4306521	0.89[EUR][1000 genomes]
rs4324141	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs4324142	0.89[EUR][1000 genomes]
rs4324143	0.89[EUR][1000 genomes]
rs4454990	0.89[CEU][hapmap];0.93[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4889225	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889227	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4889229	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4889230	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4889231	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4889233	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs5023849	0.89[EUR][1000 genomes]
rs5023850	0.86[EUR][1000 genomes]
rs5023852	0.89[EUR][1000 genomes]
rs55939311	0.87[EUR][1000 genomes]
rs56032321	0.89[EUR][1000 genomes]
rs56119129	0.89[EUR][1000 genomes]
rs56166222	0.87[EUR][1000 genomes]
rs56198248	0.80[EUR][1000 genomes]
rs56395947	0.89[EUR][1000 genomes]
rs59177227	0.89[EUR][1000 genomes]
rs59685942	0.89[EUR][1000 genomes]
rs60303302	0.82[EUR][1000 genomes]
rs61082942	0.89[EUR][1000 genomes]
rs6420419	0.89[EUR][1000 genomes]
rs6420421	0.90[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs6564819	0.82[EUR][1000 genomes]
rs7185637	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7188508	0.89[EUR][1000 genomes]
rs7203546	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7204040	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7206814	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs754429	1.00[CEU][hapmap]
rs8043855	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs8047495	0.81[EUR][1000 genomes]
rs804885	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs804895	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs804896	0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs804897	0.85[EUR][1000 genomes]
rs804902	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs804903	0.85[ASN][1000 genomes]
rs804904	0.87[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[ASN][1000 genomes]
rs804905	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8052415	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8052490	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs8056972	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs8059692	0.90[CEU][hapmap]
rs8177939	0.86[EUR][1000 genomes]
rs8177940	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs8177942	0.87[EUR][1000 genomes]
rs8177943	0.89[EUR][1000 genomes]
rs8177945	0.87[EUR][1000 genomes]
rs8177948	0.89[EUR][1000 genomes]
rs8177950	0.89[EUR][1000 genomes]
rs8177957	1.00[CEU][hapmap]
rs8177959	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs9923732	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9925940	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9925943	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs9926174	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs9929586	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9933184	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs9938965	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	esv2751615	chr16:81093099-81307599	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs935942	C16orf46	Cis_1M	lymphoblastoid	RTeQTL
rs935942	GCSH	cis	lymphoblastoid	seeQTL
rs935942	LOC100329108	cis	lymphoblastoid	seeQTL
rs935942	GCSH	cis	Muscle Skeletal	GTEx
rs935942	ATMIN	cis	Muscle Skeletal	GTEx
rs935942	C16orf61	cis	cerebellum	SCAN
rs935942	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs935942	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs935942	CENPN	cis	parietal	SCAN
rs935942	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81111400-81114000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr16:81111400-81114800	Weak transcription	Fetal Lung	lung
3	chr16:81111400-81115000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr16:81111400-81116800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr16:81111400-81117200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr16:81111400-81122400	Weak transcription	Lung	lung
7	chr16:81111400-81122600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr16:81111400-81122800	Weak transcription	Ovary	ovary
9	chr16:81111400-81128200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr16:81111400-81128400	Weak transcription	Aorta	Aorta
11	chr16:81111400-81128800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr16:81111400-81128800	Weak transcription	Psoas Muscle	Psoas
13	chr16:81111400-81128800	Weak transcription	NHDF-Ad	bronchial
14	chr16:81111400-81129000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr16:81111400-81129000	Weak transcription	Gastric	stomach
16	chr16:81111400-81129200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr16:81111600-81112400	Enhancers	K562	blood
18	chr16:81111600-81113800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr16:81111600-81114000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:81111600-81114600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:81111600-81114800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr16:81111600-81114800	Weak transcription	A549	lung
23	chr16:81111600-81115000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr16:81111600-81115200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr16:81111600-81115400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr16:81111600-81116800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr16:81111600-81116800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr16:81111600-81116800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr16:81111600-81116800	Weak transcription	Adipose Nuclei	Adipose
30	chr16:81111600-81116800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr16:81111600-81116800	Weak transcription	Fetal Stomach	stomach
32	chr16:81111600-81117200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr16:81111600-81117400	Weak transcription	Spleen	Spleen
34	chr16:81111600-81117600	Weak transcription	Fetal Intestine Small	intestine
35	chr16:81111600-81119200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr16:81111600-81120200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr16:81111600-81120800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr16:81111600-81122000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr16:81111600-81122200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr16:81111600-81122400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr16:81111600-81122400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr16:81111600-81122400	Weak transcription	Fetal Intestine Large	intestine
43	chr16:81111600-81122400	Weak transcription	NHEK	skin
44	chr16:81111600-81122800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr16:81111600-81122800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr16:81111600-81123000	Weak transcription	Primary T cells from cord blood	blood
47	chr16:81111600-81123000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr16:81111600-81123000	Weak transcription	HMEC	breast
49	chr16:81111600-81123200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr16:81111600-81123200	Weak transcription	Placenta	Placenta

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