Variant report

Variant	rs2602431
Chromosome Location	chr16:81070697-81070698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:81068857-81071180	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr16:81070200-81070796	MCF10A-Er-Src	breast:	n/a	n/a
3	HCFC1	chr16:81068860-81070884	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr16:81069096-81070711	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr16:81069248-81070708	Hela-S3	cervix:	n/a	n/a
6	ATF1	chr16:81070644-81070935	K562	blood:	n/a	n/a
7	MAX	chr16:81070509-81071095	K562	blood:	n/a	n/a
8	YY1	chr16:81070547-81070815	K562	blood:	n/a	n/a
9	MAFK	chr16:81070687-81070954	HepG2	liver:	n/a	n/a
10	POLR2A	chr16:81070482-81070898	K562	blood:	n/a	n/a
11	TEAD4	chr16:81070171-81071061	K562	blood:	n/a	n/a
12	CEBPB	chr16:81070008-81071044	K562	blood:	n/a	chr16:81070188-81070199 chr16:81070187-81070198
13	ESRRA	chr16:81068955-81070833	GM12878	blood:	n/a	n/a
14	MXI1	chr16:81068735-81071186	SK-N-SH	brain:	n/a	n/a
15	CEBPB	chr16:81069788-81070933	Hela-S3	cervix:	n/a	chr16:81070188-81070199 chr16:81070187-81070198
16	REST	chr16:81068973-81070723	H1-neurons	neurons:	n/a	chr16:81069913-81069931 chr16:81069933-81069946
17	CTCF	chr16:81068844-81070964	A549	lung:	n/a	chr16:81069997-81070010 chr16:81069952-81069965 chr16:81069291-81069307 chr16:81069272-81069280
18	SMC3	chr16:81070643-81070786	Hela-S3	cervix:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:81068890..81071040-chr16:81770218..81773249,4	MCF-7	breast:
2	chr16:81038105..81044923-chr16:81066300..81070952,14	MCF-7	breast:
3	chr16:81067084..81072191-chr16:81106033..81112629,21	MCF-7	breast:
4	chr16:81068163..81070898-chr16:81108747..81112001,7	MCF-7	breast:
5	chr16:81061882..81066764-chr16:81067446..81071538,9	MCF-7	breast:
6	chr16:81067728..81071580-chr16:81109086..81113987,13	K562	blood:
7	chr16:81069395..81071569-chr16:81120451..81122846,2	K562	blood:
8	chr16:81066967..81071215-chr16:81128766..81132498,3	MCF-7	breast:
9	chr16:81068207..81071925-chr16:81073357..81079831,13	MCF-7	breast:
10	chr16:81056423..81058180-chr16:81069392..81072113,2	MCF-7	breast:
11	chr16:81052685..81055352-chr16:81069386..81070952,2	MCF-7	breast:
12	chr16:81037151..81044642-chr16:81065528..81070966,16	K562	blood:
13	chr16:81037151..81042784-chr16:81066438..81073797,14	K562	blood:
14	chr16:81069108..81070906-chr16:81231938..81234335,3	MCF-7	breast:
15	chr16:81056962..81059865-chr16:81068197..81070898,3	K562	blood:
16	chr16:81037996..81043724-chr16:81066407..81071400,11	MCF-7	breast:
17	chr16:81067878..81071089-chr16:81109086..81112093,6	K562	blood:
18	chr16:81068173..81071730-chr16:81126382..81131671,6	MCF-7	breast:
19	chr16:81067967..81070895-chr16:81477501..81479169,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260213	TF binding region
ATMIN	TF binding region
ENSG00000166451	Chromatin interaction
ENSG00000140905	Chromatin interaction
ENSG00000261061	Chromatin interaction
ENSG00000197943	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000166473	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000260643	Chromatin interaction
ENSG00000261218	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000153815	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000166454	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11150337	0.91[ASN][1000 genomes]
rs11863158	0.85[ASN][1000 genomes]
rs11865207	0.88[ASN][1000 genomes]
rs12448368	0.85[CEU][hapmap]
rs12927239	0.89[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.89[ASN][1000 genomes]
rs12927828	0.88[ASN][1000 genomes]
rs12928556	0.81[ASN][1000 genomes]
rs12928638	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs12929903	0.81[ASN][1000 genomes]
rs12935418	0.89[ASN][1000 genomes]
rs13185	0.94[ASW][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2257378	0.85[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278025	0.82[ASN][1000 genomes]
rs2549891	0.83[MEX][hapmap]
rs2549895	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2549896	0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs2549899	0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.81[EUR][1000 genomes]
rs2602401	0.80[CHD][hapmap]
rs2602402	0.89[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2602404	0.87[ASN][1000 genomes]
rs2602407	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs2602424	0.80[YRI][hapmap]
rs2873310	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2970076	0.88[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.88[ASN][1000 genomes]
rs2970077	0.90[TSI][hapmap]
rs3743503	0.85[CEU][hapmap]
rs4454990	0.81[MEX][hapmap]
rs4889225	0.83[CHB][hapmap];0.89[CHD][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs4889229	0.82[ASN][1000 genomes]
rs4889230	0.82[ASN][1000 genomes]
rs62054589	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7188549	0.83[EUR][1000 genomes]
rs7195459	0.83[EUR][1000 genomes]
rs7203546	0.81[ASN][1000 genomes]
rs7206814	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs804885	0.82[CHB][hapmap];0.92[CHD][hapmap];0.85[MKK][hapmap];0.85[ASN][1000 genomes]
rs804896	0.84[ASN][1000 genomes]
rs804902	0.84[ASN][1000 genomes]
rs804904	0.88[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs804905	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs889516	0.86[ASN][1000 genomes]
rs935942	0.86[CHD][hapmap];0.88[MEX][hapmap]

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	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
13	esv3374530	chr16:81068676-81071224	Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	esv1820959	chr16:81069247-81070697	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2602431	CENPN	cis	multi-tissue	Pritchard
rs2602431	CENPN	cis	parietal	SCAN
rs2602431	GCSH	cis	Muscle Skeletal	GTEx
rs2602431	CENPN	cis	lymphoblastoid	seeQTL
rs2602431	CENPN	cis	brain	seeQTL
rs2602431	DC13	cis	multi-tissue	Pritchard
rs2602431	LOC100329108	cis	lymphoblastoid	seeQTL
rs2602431	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs2602431	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs2602431	BM039	cis	multi-tissue	Pritchard
rs2602431	GCSH	cis	brain	seeQTL
rs2602431	ATMIN	cis	Muscle Skeletal	GTEx
rs2602431	CENPN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81068800-81071200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr16:81069000-81070800	Active TSS	Psoas Muscle	Psoas
3	chr16:81069200-81070800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr16:81069200-81070800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr16:81069200-81071000	Active TSS	H1 Cell Line	embryonic stem cell
6	chr16:81069200-81071000	Active TSS	Colonic Mucosa	Colon
7	chr16:81069400-81070800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:81069400-81070800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr16:81069400-81070800	Active TSS	Left Ventricle	heart
10	chr16:81069400-81071000	Active TSS	Right Ventricle	heart
11	chr16:81069600-81070800	Active TSS	HSMMtube	muscle
12	chr16:81069600-81071000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr16:81069600-81071200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr16:81070000-81070800	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr16:81070000-81070800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr16:81070000-81070800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr16:81070000-81070800	Flanking Active TSS	Fetal Thymus	thymus
18	chr16:81070000-81071000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr16:81070000-81071000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr16:81070000-81071200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr16:81070200-81070800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr16:81070200-81070800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr16:81070200-81070800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr16:81070200-81070800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr16:81070200-81070800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr16:81070200-81070800	Flanking Active TSS	Liver	Liver
27	chr16:81070200-81070800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr16:81070200-81070800	Flanking Active TSS	Fetal Brain Male	brain
29	chr16:81070200-81070800	Flanking Active TSS	Fetal Brain Female	brain
30	chr16:81070200-81070800	Flanking Active TSS	Fetal Heart	heart
31	chr16:81070200-81070800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
32	chr16:81070200-81070800	Flanking Active TSS	Fetal Lung	lung
33	chr16:81070200-81070800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr16:81070200-81071000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr16:81070200-81071000	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr16:81070200-81071000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr16:81070200-81071000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr16:81070200-81071000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr16:81070200-81071000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr16:81070200-81071000	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr16:81070200-81071000	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr16:81070200-81071000	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr16:81070200-81071000	Flanking Active TSS	HUVEC	blood vessel
44	chr16:81070200-81071000	Flanking Active TSS	NHDF-Ad	bronchial
45	chr16:81070200-81071000	Flanking Active TSS	Osteobl	bone
46	chr16:81070200-81071200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr16:81070200-81071200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr16:81070200-81071200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr16:81070200-81071200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr16:81070200-81071200	Flanking Active TSS	Duodenum Mucosa	Duodenum

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