Variant report

Variant	rs56389935
Chromosome Location	chr4:119683571-119683572
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr4:119682452-119684542	SK-N-SH	brain:	n/a	chr4:119684003-119684012 chr4:119683269-119683276
2	GATA3	chr4:119682959-119683755	SH-SY5Y	brain:	n/a	chr4:119683269-119683276
3	TCF12	chr4:119682468-119684558	SK-N-SH	brain:	n/a	n/a
4	GATA2	chr4:119683290-119683664	SH-SY5Y	brain:	n/a	n/a
5	TEAD4	chr4:119682571-119683583	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr4:119682452-119683643	SK-N-SH	brain:	n/a	n/a
7	EP300	chr4:119682703-119683712	SK-N-SH_RA	brain:	n/a	n/a
8	EP300	chr4:119682657-119683662	SK-N-SH_RA	brain:	n/a	n/a
9	EP300	chr4:119682427-119685460	SK-N-SH	brain:	n/a	chr4:119684666-119684680 chr4:119684444-119684458 chr4:119684382-119684396 chr4:119683726-119683735
10	GATA3	chr4:119682648-119683580	SK-N-SH	brain:	n/a	chr4:119683269-119683276
11	NFIC	chr4:119682503-119684571	SK-N-SH	brain:	n/a	chr4:119683935-119683963

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119682565..119685004-chr4:119691395..119693474,2	K562	blood:
2	chr4:119663074..119665323-chr4:119683006..119685125,2	K562	blood:

Variant related genes	Relation type
SEC24D	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10001115	0.88[EUR][1000 genomes]
rs10018977	0.88[EUR][1000 genomes]
rs10019311	0.88[EUR][1000 genomes]
rs10025640	0.88[EUR][1000 genomes]
rs11098451	0.95[EUR][1000 genomes]
rs11931194	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11938970	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17257945	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17258050	0.91[AMR][1000 genomes]
rs17258106	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17258830	0.88[EUR][1000 genomes]
rs17258907	1.00[AFR][1000 genomes]
rs17259173	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17259257	1.00[AFR][1000 genomes]
rs17259284	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17323012	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17323034	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17323877	0.91[AMR][1000 genomes]
rs17324807	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17324821	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17324884	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17324968	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17325017	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17325129	0.88[EUR][1000 genomes]
rs17325192	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs28595532	0.95[EUR][1000 genomes]
rs28600971	0.95[EUR][1000 genomes]
rs28627331	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28797314	0.88[EUR][1000 genomes]
rs28837152	0.88[EUR][1000 genomes]
rs41455648	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55633605	0.88[EUR][1000 genomes]
rs55634130	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55640619	0.88[EUR][1000 genomes]
rs55649377	0.88[EUR][1000 genomes]
rs55668908	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs55671478	0.88[EUR][1000 genomes]
rs55704595	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs55726697	0.88[EUR][1000 genomes]
rs55744948	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs55758547	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs55794497	0.88[EUR][1000 genomes]
rs55806110	0.88[EUR][1000 genomes]
rs55823625	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs55845920	1.00[AFR][1000 genomes]
rs55869953	0.88[EUR][1000 genomes]
rs55901549	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs55913633	0.88[EUR][1000 genomes]
rs55985953	0.88[EUR][1000 genomes]
rs55990797	1.00[AFR][1000 genomes]
rs56000725	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56027489	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56042726	0.82[EUR][1000 genomes]
rs56046449	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56046676	0.88[EUR][1000 genomes]
rs56055826	1.00[AFR][1000 genomes]
rs56104443	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56117870	0.84[EUR][1000 genomes]
rs56124677	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56144225	1.00[AFR][1000 genomes]
rs56150431	0.88[EUR][1000 genomes]
rs56162974	0.88[EUR][1000 genomes]
rs56200441	1.00[AFR][1000 genomes]
rs56212415	0.88[EUR][1000 genomes]
rs56225646	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56227053	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56252481	0.88[EUR][1000 genomes]
rs56264833	0.84[EUR][1000 genomes]
rs56283736	0.88[EUR][1000 genomes]
rs56291421	0.88[EUR][1000 genomes]
rs56302493	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56302600	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56303276	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56309519	0.88[EUR][1000 genomes]
rs56322132	0.88[EUR][1000 genomes]
rs56331118	0.88[EUR][1000 genomes]
rs56342843	0.88[EUR][1000 genomes]
rs56359736	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56364904	0.88[EUR][1000 genomes]
rs56388366	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56762141	0.88[EUR][1000 genomes]
rs6818519	0.88[EUR][1000 genomes]
rs73842212	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73842253	0.88[EUR][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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats 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	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
3	chr4:119640800-119692600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:119649200-119687600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:119649200-119693600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:119651800-119687400	Weak transcription	Thymus	Thymus
7	chr4:119654400-119687400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:119659600-119690400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:119660400-119688200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:119660400-119689800	Weak transcription	Brain Angular Gyrus	brain
11	chr4:119661800-119684600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:119662000-119687600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:119662000-119694400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:119665200-119687600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:119665800-119687400	Weak transcription	Spleen	Spleen
16	chr4:119668000-119683600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:119668000-119689800	Weak transcription	Brain Germinal Matrix	brain
18	chr4:119668200-119684000	Weak transcription	K562	blood
19	chr4:119668200-119690200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:119673000-119687400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:119673000-119687400	Weak transcription	Pancreas	Pancrea
22	chr4:119673200-119687400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:119673400-119684600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:119673400-119687400	Weak transcription	Fetal Thymus	thymus
25	chr4:119673400-119687600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:119673400-119688000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr4:119673400-119688600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:119673600-119684000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:119673600-119685000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr4:119674000-119684800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:119674000-119685200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:119675400-119685600	Strong transcription	NH-A	brain
33	chr4:119675400-119686600	Weak transcription	Brain Substantia Nigra	brain
34	chr4:119675600-119685400	Weak transcription	Aorta	Aorta
35	chr4:119675800-119686800	Weak transcription	Stomach Mucosa	stomach
36	chr4:119675800-119687800	Weak transcription	Psoas Muscle	Psoas
37	chr4:119677000-119688800	Genic enhancers	Osteobl	bone
38	chr4:119678000-119685000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:119678000-119685200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:119678000-119685400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:119678000-119689400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:119678200-119692000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr4:119678400-119687400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:119678600-119684000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:119678600-119684600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr4:119678600-119685000	Weak transcription	Left Ventricle	heart
47	chr4:119678600-119687400	Weak transcription	Gastric	stomach
48	chr4:119678600-119687400	Weak transcription	Lung	lung
49	chr4:119678600-119687600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:119678600-119687800	Weak transcription	Right Atrium	heart

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