Variant report

Variant	rs12501006
Chromosome Location	chr4:56503519-56503520
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:56503017-56503773	K562	blood:	n/a	n/a
2	EGR1	chr4:56503339-56503680	K562	blood:	n/a	n/a
3	TBL1XR1	chr4:56503510-56503984	K562	blood:	n/a	n/a
4	ZBTB7A	chr4:56503364-56503618	K562	blood:	n/a	n/a
5	TBP	chr4:56503340-56503875	K562	blood:	n/a	n/a
6	POLR2A	chr4:56503231-56503717	K562	blood:	n/a	n/a
7	REST	chr4:56503341-56503647	K562	blood:	n/a	n/a
8	RCOR1	chr4:56500802-56503942	K562	blood:	n/a	n/a
9	MAX	chr4:56503434-56503700	K562	blood:	n/a	n/a
10	REST	chr4:56500830-56504009	H1-neurons	neurons:	n/a	chr4:56502226-56502236
11	ZNF143	chr4:56503342-56503706	K562	blood:	n/a	n/a
12	POLR2A	chr4:56503309-56503755	K562	blood:	n/a	n/a
13	POLR2A	chr4:56499394-56503785	K562	blood:	n/a	n/a
14	RXRA	chr4:56503380-56503648	H1-hESC	embryonic stem cell:	n/a	n/a
15	JUND	chr4:56503308-56503817	K562	blood:	n/a	n/a
16	TAF7	chr4:56503485-56503607	K562	blood:	n/a	n/a
17	ZMIZ1	chr4:56502307-56503969	K562	blood:	n/a	n/a
18	EGR1	chr4:56503274-56503722	K562	blood:	n/a	n/a
19	IRF1	chr4:56503287-56503901	K562	blood:	n/a	n/a
20	TBL1XR1	chr4:56503434-56503915	K562	blood:	n/a	n/a
21	TEAD4	chr4:56502158-56503849	K562	blood:	n/a	n/a
22	POLR2A	chr4:56503294-56503592	K562	blood:	n/a	n/a
23	POLR2A	chr4:56503194-56503645	H1-neurons	neurons:	n/a	n/a
24	MYC	chr4:56501384-56503906	K562	blood:	n/a	chr4:56502207-56502216 chr4:56502071-56502080
25	EP300	chr4:56502323-56504583	K562	blood:	n/a	chr4:56504418-56504432
26	POLR2A	chr4:56503179-56503614	H1-neurons	neurons:	n/a	n/a
27	MAZ	chr4:56503331-56503965	K562	blood:	n/a	n/a
28	POLR2A	chr4:56501413-56503915	K562	blood:	n/a	n/a
29	ARID3A	chr4:56503388-56504015	K562	blood:	n/a	n/a
30	POLR2A	chr4:56499543-56503922	K562	blood:	n/a	n/a
31	MAX	chr4:56503342-56503584	K562	blood:	n/a	n/a
32	MAX	chr4:56503412-56503632	K562	blood:	n/a	n/a
33	POLR2A	chr4:56499874-56503767	K562	blood:	n/a	n/a
34	NR2F2	chr4:56503282-56504657	K562	blood:	n/a	n/a
35	YY1	chr4:56503338-56503648	K562	blood:	n/a	n/a
36	NR2F2	chr4:56503390-56503840	K562	blood:	n/a	n/a
37	POLR2A	chr4:56499765-56503986	K562	blood:	n/a	n/a
38	MYC	chr4:56503386-56503826	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:56211245..56214093-chr4:56502603..56505420,3	K562	blood:
2	chr4:56410839..56413778-chr4:56501227..56505067,4	K562	blood:
3	chr4:56408119..56414507-chr4:56501105..56505595,8	K562	blood:
4	chr4:56411599..56413538-chr4:56502547..56504625,2	MCF-7	breast:

No data

Variant related genes	Relation type
NMU	TF binding region
ENSG00000134852	Chromatin interaction
ENSG00000272969	Chromatin interaction
ENSG00000128039	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11133406	0.84[EUR][1000 genomes]
rs11722402	0.84[EUR][1000 genomes]
rs11723011	0.84[EUR][1000 genomes]
rs11727450	0.84[EUR][1000 genomes]
rs11728776	0.86[EUR][1000 genomes]
rs11729111	0.84[EUR][1000 genomes]
rs11734493	0.84[EUR][1000 genomes]
rs11735358	0.83[EUR][1000 genomes]
rs11735815	0.84[EUR][1000 genomes]
rs12499085	0.86[EUR][1000 genomes]
rs12500147	0.86[EUR][1000 genomes]
rs12503046	0.86[EUR][1000 genomes]
rs12503479	0.84[EUR][1000 genomes]
rs12506506	0.86[EUR][1000 genomes]
rs12507525	0.86[EUR][1000 genomes]
rs12508869	0.86[EUR][1000 genomes]
rs12509559	0.90[EUR][1000 genomes]
rs2412668	0.84[EUR][1000 genomes]
rs35256215	0.84[EUR][1000 genomes]
rs55665531	0.84[EUR][1000 genomes]
rs55885309	0.88[EUR][1000 genomes]
rs56096459	0.84[EUR][1000 genomes]
rs56260406	0.90[EUR][1000 genomes]
rs73236166	0.84[EUR][1000 genomes]
rs73236167	0.82[EUR][1000 genomes]
rs73236168	0.84[EUR][1000 genomes]
rs73236171	0.90[EUR][1000 genomes]
rs73236173	0.88[EUR][1000 genomes]
rs73236174	0.87[EUR][1000 genomes]
rs73236175	0.87[EUR][1000 genomes]
rs73236178	0.86[EUR][1000 genomes]
rs73236179	0.86[EUR][1000 genomes]
rs73236181	0.86[EUR][1000 genomes]
rs73236182	0.83[EUR][1000 genomes]
rs73236183	0.84[EUR][1000 genomes]
rs73236184	0.84[EUR][1000 genomes]
rs73236185	0.84[EUR][1000 genomes]
rs73236186	0.84[EUR][1000 genomes]
rs73236187	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv998179	chr4:56425126-56694339	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv932636	chr4:56438618-56667329	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv879021	chr4:56482750-56648713	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3393088	chr4:56484073-56503988	Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv3395811	chr4:56486113-56514675	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3406771	chr4:56501220-56503968	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12501006	NMU	cis	Thyroid	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56501400-56503600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr4:56501600-56503600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr4:56501800-56503800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr4:56502600-56503800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:56502800-56503800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:56502800-56504000	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr4:56503000-56503600	Bivalent Enhancer	Fetal Brain Male	brain
8	chr4:56503000-56503600	Enhancers	HMEC	breast
9	chr4:56503000-56503800	Bivalent Enhancer	Fetal Lung	lung
10	chr4:56503000-56503800	Bivalent Enhancer	Fetal Stomach	stomach
11	chr4:56503000-56504200	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr4:56503200-56503600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:56503200-56503600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:56503200-56503600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:56503200-56503600	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr4:56503200-56503800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:56503200-56503800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
18	chr4:56503200-56503800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:56503200-56504000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:56503200-56504200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:56503200-56504200	Weak transcription	Spleen	Spleen
22	chr4:56503200-56504600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:56503400-56503600	Active TSS	H1 Cell Line	embryonic stem cell
24	chr4:56503400-56503600	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr4:56503400-56503600	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr4:56503400-56503600	Enhancers	Brain Germinal Matrix	brain
27	chr4:56503400-56503600	Enhancers	K562	blood
28	chr4:56503400-56503800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr4:56503400-56503800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:56503400-56503800	Active TSS	Fetal Kidney	kidney
31	chr4:56503400-56504000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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