Variant report

Variant	rs12420958
Chromosome Location	chr11:17100432-17100433
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:61)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:17098648-17100585	K562	blood:	n/a	n/a
2	UBTF	chr11:17098948-17100483	K562	blood:	n/a	n/a
3	POLR2A	chr11:17093738-17102258	K562	blood:	n/a	n/a
4	TAF1	chr11:17100215-17100450	K562	blood:	n/a	n/a
5	POLR2A	chr11:17093851-17100645	GM12878	blood:	n/a	n/a
6	POLR2A	chr11:17100200-17100485	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:17098128-17100520	GM19193	blood:	n/a	n/a
8	POLR2A	chr11:17097758-17100562	H1-hESC	embryonic stem cell:	n/a	n/a
9	YY1	chr11:17098809-17100534	K562	blood:	n/a	n/a
10	POLR2A	chr11:17096761-17100592	HepG2	liver:	n/a	n/a
11	POLR2A	chr11:17094537-17100702	K562	blood:	n/a	n/a
12	POLR2A	chr11:17092732-17100728	GM12891	blood:	n/a	n/a
13	POLR2A	chr11:17094536-17100574	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr11:17097215-17100753	K562	blood:	n/a	n/a
15	POLR2A	chr11:17096094-17100723	K562	blood:	n/a	n/a
16	ZNF384	chr11:17099029-17100726	K562	blood:	n/a	n/a
17	POLR2A	chr11:17097800-17100526	K562	blood:	n/a	n/a
18	POLR2A	chr11:17096026-17100607	GM18505	blood:	n/a	n/a
19	YY1	chr11:17100239-17100482	GM12878	blood:	n/a	n/a
20	MXI1	chr11:17097588-17100750	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr11:17097411-17100595	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr11:17098057-17100540	K562	blood:	n/a	n/a
23	HEY1	chr11:17097750-17100479	K562	blood:	n/a	chr11:17099680-17099695
24	YY1	chr11:17100245-17100451	K562	blood:	n/a	n/a
25	POLR2A	chr11:17092645-17100693	SK-N-MC	brain:	n/a	n/a
26	MAX	chr11:17098709-17100523	K562	blood:	n/a	chr11:17099128-17099138

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:17100390-17100440	HRE	kidney:	n/a
2	chr11:17100390-17100440	AG04450	lung:	fetal
3	chr11:17100390-17100440	GM12891	blood:	n/a
4	chr11:17100390-17100440	HepG2	liver:	n/a
5	chr11:17100390-17100440	PFSK-1	brain:	n/a
6	chr11:17100390-17100440	LNCaP	prostate:	n/a
7	chr11:17100390-17100440	T-47D	breast:	n/a
8	chr11:17100390-17100440	HCF	heart:	n/a
9	chr11:17100390-17100440	A549	lung:	n/a
10	chr11:17100390-17100440	HEEpiC	esophagus:	n/a
11	chr11:17100390-17100440	GM12878	blood:	n/a
12	chr11:17100390-17100440	SK-N-SH	brain:	n/a
13	chr11:17100390-17100440	MCF10A-Er-Src	breast:	n/a
14	chr11:17100390-17100440	ProgFib	skin:	n/a
15	chr11:17100390-17100440	HNPCEpiC	eye:	n/a
16	chr11:17100390-17100440	NHDF-neo	bronchial:	n/a
17	chr11:17100390-17100440	AG04449	skin:	fetal
18	chr11:17100390-17100440	HCM	heart:	n/a
19	chr11:17100390-17100440	HPAEpiC	pulmonary alveolar:	n/a
20	chr11:17100390-17100440	RPTEC	kidney:	n/a
21	chr11:17100390-17100440	Hepatocyte	liver:	n/a
22	chr11:17100390-17100440	BE2_C	brain:	n/a
23	chr11:17100390-17100440	HEK293	kidney:	embryo
24	chr11:17100390-17100440	K562	blood:	n/a
25	chr11:17100390-17100440	AG10803	skin:	n/a
26	chr11:17100390-17100440	HUVEC	blood vessel:	n/a
27	chr11:17100390-17100440	AoSMC	blood vessel:	n/a
28	chr11:17100390-17100440	U87	brain:	n/a
29	chr11:17100390-17100440	H1-hESC	embryonic stem cell:	embryo
30	chr11:17100390-17100440	Caco-2	colon:	n/a
31	chr11:17100390-17100440	BJ	skin:	n/a
32	chr11:17100390-17100440	HCT-116	colon:	n/a
33	chr11:17100390-17100440	SKMC	muscle:	n/a
34	chr11:17100390-17100440	ECC-1	luminal epithelium:	n/a
35	chr11:17100390-17100440	NB4	blood:	n/a
36	chr11:17100390-17100440	HL-60	blood:	n/a
37	chr11:17100390-17100440	NHBE	bronchial:	n/a
38	chr11:17100390-17100440	CMK	blood:	n/a
39	chr11:17100390-17100440	HMEC	breast:	n/a
40	chr11:17100390-17100440	MCF-7	breast:	n/a
41	chr11:17100390-17100440	HCPEpiC	choroid plexus:	n/a
42	chr11:17100390-17100440	SK-N-SH_RA	brain:	n/a
43	chr11:17100390-17100440	PrEC	prostate:	n/a
44	chr11:17100390-17100440	HAEpiC	amniotic membrane:	n/a
45	chr11:17100390-17100440	GM19239	blood:	n/a
46	chr11:17100390-17100440	ovcar-3	ovarian:	n/a
47	chr11:17100390-17100440	SK-N-MC	brain:	n/a
48	chr11:17100390-17100440	NT2-D1	testis:	n/a
49	chr11:17100390-17100440	Hela-S3	cervix:	n/a
50	chr11:17100390-17100440	AG09309	skin:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr11:16804738..16808801-chr11:17097608..17100627,5	K562	blood:
2	chr11:17099350..17101330-chr11:17109097..17111339,2	K562	blood:
3	chr11:16759714..16762827-chr11:17097720..17101099,4	K562	blood:
4	chr11:17097827..17101102-chr11:17296839..17299555,4	K562	blood:
5	chr11:17097769..17100478-chr3:143690055..143692307,2	MCF-7	breast:
6	chr11:17097070..17101102-chr11:17296326..17299484,3	K562	blood:
7	chr11:17027622..17030583-chr11:17098379..17100590,2	K562	blood:
8	chr11:16759176..16761906-chr11:17098692..17100616,2	MCF-7	breast:
9	chr11:17096429..17100576-chr11:17227768..17230724,6	K562	blood:
10	chr11:17099951..17102029-chr11:17121087..17123839,2	MCF-7	breast:
11	chr11:17099995..17101561-chr11:17159735..17162103,2	K562	blood:
12	chr11:16960761..16963314-chr11:17099363..17101117,2	MCF-7	breast:
13	chr11:17097208..17101887-chr11:17227768..17230798,9	K562	blood:
14	chr11:17098478..17100931-chr17:59476241..59478619,2	MCF-7	breast:
15	chr11:17097048..17102595-chr11:17228016..17231208,7	MCF-7	breast:
16	chr11:17008798..17010671-chr11:17099542..17102207,2	MCF-7	breast:
17	chr11:17099359..17101768-chr11:17550989..17553473,2	K562	blood:
18	chr11:17099339..17100906-chr17:80692924..80694500,2	MCF-7	breast:
19	chr11:17097742..17101154-chr11:17227974..17231312,6	MCF-7	breast:

No data

Variant related genes	Relation type
RPS13	TF binding region
SNORD14A	TF binding region
SNORD14B	TF binding region
RPS13	CpG island
SNORD14B	CpG island
SNORD14A	CpG island
ENSG00000110693	Chromatin interaction
ENSG00000110696	Chromatin interaction
ENSG00000266493	Chromatin interaction
ENSG00000166689	Chromatin interaction
ENSG00000167363	Chromatin interaction
ENSG00000011405	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000070081	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000181744	Chromatin interaction
ENSG00000240808	Chromatin interaction
ENSG00000267131	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10832731	0.91[EUR][1000 genomes]
rs11024149	0.90[EUR][1000 genomes]
rs11024151	0.86[EUR][1000 genomes]
rs11608038	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1236311	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12575466	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12577388	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12577418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794156	0.86[ASN][1000 genomes]
rs17472942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17560341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561348	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17641418	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1987694	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs214903	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs214932	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs214933	0.87[EUR][1000 genomes]
rs214934	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs214938	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34724588	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34941502	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3950680	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs476890	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs492263	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs522619	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56030184	0.85[ASN][1000 genomes]
rs569780	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs586785	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs615424	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61879692	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644419	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs664382	0.87[EUR][1000 genomes]
rs665311	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs679201	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7108067	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7478986	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12420958	NUCB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17097600-17100600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:17097800-17100600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:17098400-17100600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr11:17098400-17100600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:17098400-17100600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:17098400-17100800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr11:17098600-17100600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:17098600-17100600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:17098600-17100600	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr11:17098600-17100600	Active TSS	HMEC	breast
11	chr11:17098600-17100600	Active TSS	HSMM	muscle
12	chr11:17098600-17100600	Active TSS	HUVEC	blood vessel
13	chr11:17098600-17100800	Active TSS	GM12878-XiMat	blood
14	chr11:17098800-17100600	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr11:17098800-17100800	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr11:17099000-17100600	Active TSS	Brain Germinal Matrix	brain
17	chr11:17099200-17100600	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr11:17099400-17100600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:17099400-17100600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:17099400-17100600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr11:17099400-17100600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr11:17099400-17100800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr11:17099800-17100600	Flanking Active TSS	Thymus	Thymus
24	chr11:17100000-17100600	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr11:17100000-17100600	Flanking Active TSS	Fetal Thymus	thymus
26	chr11:17100000-17100800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:17100000-17100800	Flanking Active TSS	Dnd41	blood
28	chr11:17100000-17101200	Active TSS	Placenta	Placenta
29	chr11:17100000-17110800	Weak transcription	Stomach Mucosa	stomach
30	chr11:17100000-17111200	Weak transcription	Aorta	Aorta
31	chr11:17100000-17112800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr11:17100000-17112800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr11:17100200-17100600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
34	chr11:17100200-17100600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:17100200-17100600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr11:17100200-17100600	Enhancers	Primary B cells from peripheral blood	blood
37	chr11:17100200-17100600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr11:17100200-17100600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr11:17100200-17100600	Active TSS	Adipose Nuclei	Adipose
40	chr11:17100200-17100600	Enhancers	Liver	Liver
41	chr11:17100200-17100600	Enhancers	Brain Substantia Nigra	brain
42	chr11:17100200-17100600	Enhancers	Fetal Brain Male	brain
43	chr11:17100200-17100600	Enhancers	Fetal Muscle Trunk	muscle
44	chr11:17100200-17100600	Enhancers	Lung	lung
45	chr11:17100200-17100600	Enhancers	Small Intestine	intestine
46	chr11:17100200-17100600	Enhancers	Spleen	Spleen
47	chr11:17100200-17100600	Enhancers	HepG2	liver
48	chr11:17100200-17108000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr11:17100200-17109000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr11:17100200-17109400	Weak transcription	Colon Smooth Muscle	Colon

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