Variant report

Variant	rs1488937
Chromosome Location	chr4:56501534-56501535
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr4:56500956-56501829	K562	blood:	n/a	n/a
2	POLR2A	chr4:56501395-56501952	H1-neurons	neurons:	n/a	n/a
3	MAX	chr4:56501398-56501860	K562	blood:	n/a	n/a
4	ARID3A	chr4:56501495-56501827	K562	blood:	n/a	n/a
5	KAP1	chr4:56501181-56502402	HEK293	kidney:	n/a	chr4:56502123-56502131
6	TBL1XR1	chr4:56499512-56501926	K562	blood:	n/a	n/a
7	POLR2A	chr4:56501200-56503215	K562	blood:	n/a	n/a
8	EP300	chr4:56501150-56501964	K562	blood:	n/a	chr4:56501233-56501240
9	RCOR1	chr4:56500802-56503942	K562	blood:	n/a	n/a
10	REST	chr4:56500830-56504009	H1-neurons	neurons:	n/a	chr4:56502226-56502236
11	MAX	chr4:56501286-56501845	K562	blood:	n/a	n/a
12	HEY1	chr4:56501270-56501979	K562	blood:	n/a	n/a
13	IRF1	chr4:56500752-56501984	K562	blood:	n/a	chr4:56501094-56501106
14	MYC	chr4:56501418-56501789	K562	blood:	n/a	n/a
15	TAF1	chr4:56501417-56501788	K562	blood:	n/a	n/a
16	POLR2A	chr4:56499394-56503785	K562	blood:	n/a	n/a
17	CCNT2	chr4:56501265-56503172	K562	blood:	n/a	chr4:56501740-56501760
18	TBP	chr4:56501439-56501884	K562	blood:	n/a	n/a
19	POLR2A	chr4:56501493-56501618	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr4:56501507-56501596	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr4:56501171-56503095	K562	blood:	n/a	n/a
22	UBTF	chr4:56501387-56502973	K562	blood:	n/a	n/a
23	ATF1	chr4:56501416-56501837	K562	blood:	n/a	n/a
24	BHLHE40	chr4:56501226-56501818	K562	blood:	n/a	n/a
25	SIN3AK20	chr4:56501345-56501763	K562	blood:	n/a	n/a
26	JUN	chr4:56501517-56501958	K562	blood:	n/a	n/a
27	RCOR1	chr4:56501450-56502093	K562	blood:	n/a	n/a
28	JUND	chr4:56501293-56501879	K562	blood:	n/a	n/a
29	POLR2A	chr4:56500485-56503059	Raji	blood:	n/a	n/a
30	MYC	chr4:56501384-56503906	K562	blood:	n/a	chr4:56502207-56502216 chr4:56502071-56502080
31	IRF1	chr4:56501444-56501896	K562	blood:	n/a	n/a
32	UBTF	chr4:56500856-56503073	K562	blood:	n/a	n/a
33	GATA2	chr4:56501183-56502511	SH-SY5Y	brain:	n/a	n/a
34	TAL1	chr4:56501179-56501907	K562	blood:	n/a	chr4:56501742-56501760
35	TEAD4	chr4:56501206-56501994	K562	blood:	n/a	n/a
36	POLR2A	chr4:56501413-56503915	K562	blood:	n/a	n/a
37	POLR2A	chr4:56499543-56503922	K562	blood:	n/a	n/a
38	POLR2A	chr4:56499874-56503767	K562	blood:	n/a	n/a
39	MXI1	chr4:56500616-56503285	SK-N-SH	brain:	n/a	n/a
40	MAZ	chr4:56501304-56501869	K562	blood:	n/a	n/a
41	POLR2A	chr4:56499478-56502006	K562	blood:	n/a	n/a
42	ZNF263	chr4:56501142-56502599	HEK293-T-REx	kidney:	n/a	n/a
43	GATA3	chr4:56501403-56501717	SH-SY5Y	brain:	n/a	n/a
44	CUX1	chr4:56501303-56501923	K562	blood:	n/a	n/a
45	POLR2A	chr4:56501188-56502009	H1-neurons	neurons:	n/a	n/a
46	POLR2A	chr4:56501171-56502577	K562	blood:	n/a	n/a
47	POLR2A	chr4:56501230-56502650	K562	blood:	n/a	n/a
48	POLR2A	chr4:56499765-56503986	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:56500129..56502345-chr4:56579313..56582236,2	K562	blood:
2	chr4:56410839..56413778-chr4:56501227..56505067,4	K562	blood:
3	chr4:56408119..56414507-chr4:56501105..56505595,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMU-2	chr4:56501440-56501555	l_2648_chr4:56499345-56508927_adipose

No data

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

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10000850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56156718	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56268402	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62308711	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62308712	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62308713	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6823777	0.89[ASN][1000 genomes]
rs9999653	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][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

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56500000-56501600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:56500600-56501600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
3	chr4:56500600-56501600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
4	chr4:56500600-56501600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
5	chr4:56500600-56501800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
6	chr4:56500800-56501600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
7	chr4:56500800-56502600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
8	chr4:56501000-56501600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
9	chr4:56501000-56501600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:56501000-56501600	Transcr. at gene 5' and 3'	K562	blood
11	chr4:56501000-56503000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:56501200-56501600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:56501200-56501600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:56501200-56501600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:56501200-56501600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
16	chr4:56501200-56501600	Bivalent Enhancer	Stomach Mucosa	stomach
17	chr4:56501200-56501800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr4:56501200-56501800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:56501200-56502000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:56501200-56502000	Flanking Active TSS	NHEK	skin
21	chr4:56501200-56503200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
22	chr4:56501200-56503200	Enhancers	Spleen	Spleen
23	chr4:56501400-56501600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:56501400-56501600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
25	chr4:56501400-56501600	Bivalent Enhancer	Brain Angular Gyrus	brain
26	chr4:56501400-56501600	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
27	chr4:56501400-56501600	Bivalent/Poised TSS	Brain Substantia Nigra	brain
28	chr4:56501400-56501600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
29	chr4:56501400-56501600	Active TSS	Esophagus	oesophagus
30	chr4:56501400-56501600	Bivalent/Poised TSS	Fetal Stomach	stomach
31	chr4:56501400-56501600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
32	chr4:56501400-56501600	Enhancers	HMEC	breast
33	chr4:56501400-56501800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
34	chr4:56501400-56501800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
35	chr4:56501400-56501800	Bivalent Enhancer	Primary T cells from cord blood	blood
36	chr4:56501400-56501800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:56501400-56501800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:56501400-56501800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
39	chr4:56501400-56501800	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr4:56501400-56501800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr4:56501400-56501800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
42	chr4:56501400-56501800	Flanking Bivalent TSS/Enh	Fetal Heart	heart
43	chr4:56501400-56501800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
44	chr4:56501400-56501800	Bivalent Enhancer	Right Ventricle	heart
45	chr4:56501400-56502000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
46	chr4:56501400-56502000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
47	chr4:56501400-56502000	Bivalent Enhancer	Adipose Nuclei	Adipose
48	chr4:56501400-56502000	Bivalent Enhancer	Colon Smooth Muscle	Colon
49	chr4:56501400-56502000	Bivalent Enhancer	Fetal Muscle Leg	muscle
50	chr4:56501400-56502000	Enhancers	Gastric	stomach

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