Variant report

Variant	rs1005438
Chromosome Location	chr4:55523938-55523939
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	ZNF263	chr4:55523518-55524491	HEK293-T-REx	kidney:	n/a	chr4:55523678-55523687 chr4:55524062-55524071 chr4:55523917-55523926 chr4:55523920-55523929
2	MAX	chr4:55523080-55525348	H1-hESC	embryonic stem cell:	n/a	chr4:55523411-55523420 chr4:55524901-55524910 chr4:55524580-55524590
3	POLR2A	chr4:55523097-55525390	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr4:55523861-55524452	Gliobla	brain:	n/a	n/a
5	ZBTB7A	chr4:55523701-55524693	ECC-1	luminal epithelium:	n/a	n/a
6	MYC	chr4:55523596-55524244	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:55523761-55524501	SK-N-MC	brain:	n/a	n/a
8	KAP1	chr4:55523774-55524409	HEK293	kidney:	n/a	n/a
9	MAX	chr4:55523534-55524409	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr4:55523925-55524288	HUVEC	blood vessel:	n/a	n/a
11	TCF12	chr4:55523816-55524405	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr4:55523259-55524479	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr4:55522933-55528781	PBDE	blood:	n/a	n/a
14	E2F6	chr4:55523231-55524347	H1-hESC	embryonic stem cell:	n/a	chr4:55523901-55523915
15	ZNF143	chr4:55523759-55524396	H1-hESC	embryonic stem cell:	n/a	chr4:55523917-55523935 chr4:55524056-55524074
16	TBP	chr4:55523302-55524434	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr4:55523263-55524432	H1-hESC	embryonic stem cell:	n/a	chr4:55523411-55523420
18	ZBTB7A	chr4:55523643-55524714	ECC-1	luminal epithelium:	n/a	n/a
19	SP4	chr4:55523585-55524077	H1-hESC	embryonic stem cell:	n/a	chr4:55524027-55524043
20	POLR2A	chr4:55523850-55524357	HEK293	kidney:	n/a	n/a
21	MAX	chr4:55523208-55524664	H1-hESC	embryonic stem cell:	n/a	chr4:55523411-55523420 chr4:55524580-55524590
22	TAF7	chr4:55523691-55524372	H1-hESC	embryonic stem cell:	n/a	n/a
23	TCF12	chr4:55523785-55524013	H1-hESC	embryonic stem cell:	n/a	n/a
24	SP1	chr4:55523896-55524412	H1-hESC	embryonic stem cell:	n/a	chr4:55524060-55524074 chr4:55524029-55524041 chr4:55524030-55524040 chr4:55524029-55524041 chr4:55524030-55524040 chr4:55524063-55524075
25	HMGN3	chr4:55523638-55525245	K562	blood:	n/a	n/a
26	SIN3A	chr4:55523370-55524457	H1-hESC	embryonic stem cell:	n/a	n/a
27	TAF1	chr4:55523229-55524404	H1-hESC	embryonic stem cell:	n/a	n/a
28	E2F6	chr4:55523103-55525556	H1-hESC	embryonic stem cell:	n/a	chr4:55524860-55524872 chr4:55524863-55524872 chr4:55525284-55525296 chr4:55525287-55525296 chr4:55525073-55525083 chr4:55524579-55524588 chr4:55523901-55523915 chr4:55525090-55525101
29	RAD21	chr4:55523859-55524354	H1-hESC	embryonic stem cell:	n/a	chr4:55523972-55523986
30	ZBTB7A	chr4:55523936-55524175	K562	blood:	n/a	n/a
31	MAZ	chr4:55523902-55524398	K562	blood:	n/a	n/a
32	RAD21	chr4:55523461-55524240	H1-hESC	embryonic stem cell:	n/a	chr4:55523972-55523986
33	CCNT2	chr4:55523780-55525332	K562	blood:	n/a	chr4:55525287-55525296 chr4:55525323-55525332
34	MAX	chr4:55523505-55524484	ECC-1	luminal epithelium:	n/a	n/a
35	MAZ	chr4:55523514-55524351	IMR90	lung:	n/a	n/a
36	YY1	chr4:55523150-55524253	H1-hESC	embryonic stem cell:	n/a	chr4:55523360-55523371
37	JUND	chr4:55523101-55524284	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr4:55523245-55524400	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTBP2	chr4:55523639-55525813	H1-hESC	embryonic stem cell:	n/a	n/a
40	TAF1	chr4:55523173-55524519	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr4:55523479-55524508	H1-hESC	embryonic stem cell:	n/a	n/a
42	TEAD4	chr4:55523917-55524320	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr4:55523910-55524333	H1-neurons	neurons:	n/a	n/a
44	BACH1	chr4:55523561-55524183	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr4:55523883-55524347	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr4:55523180-55525342	H1-hESC	embryonic stem cell:	n/a	n/a
47	CHD2	chr4:55523416-55524495	H1-hESC	embryonic stem cell:	n/a	chr4:55523703-55523713 chr4:55523679-55523689

Variant related genes	Relation type
KIT	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11730497	0.80[EUR][1000 genomes]
rs11733357	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11736016	0.80[EUR][1000 genomes]
rs12512899	0.80[EUR][1000 genomes]
rs13128858	0.93[EUR][1000 genomes]
rs13138563	0.80[EUR][1000 genomes]
rs17827974	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2215726	0.80[EUR][1000 genomes]
rs2237031	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237035	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282778	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282779	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282780	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282781	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2703456	0.81[EUR][1000 genomes]
rs34284864	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35441406	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3756197	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3819387	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3819389	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3819392	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864915	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554196	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6825657	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71599647	0.82[EUR][1000 genomes]
rs759082	0.81[EUR][1000 genomes]
rs759083	0.93[EUR][1000 genomes]
rs7655556	0.82[EUR][1000 genomes]
rs7655588	0.82[EUR][1000 genomes]
rs7656858	0.82[EUR][1000 genomes]
rs7675203	0.81[EUR][1000 genomes]
rs7684000	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7697799	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv997430	chr4:55253397-55529288	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1010702	chr4:55440944-55528450	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55523000-55524600	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr4:55523000-55525600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:55523000-55525800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
4	chr4:55523000-55526200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:55523000-55528600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:55523200-55524200	Active TSS	Fetal Brain Female	brain
7	chr4:55523200-55524600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:55523200-55524600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:55523200-55524600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
10	chr4:55523200-55525400	Active TSS	Brain Substantia Nigra	brain
11	chr4:55523200-55525800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr4:55523200-55526400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:55523400-55524000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:55523400-55524000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
15	chr4:55523400-55524000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
16	chr4:55523400-55524000	Active TSS	Right Ventricle	heart
17	chr4:55523400-55524000	Flanking Bivalent TSS/Enh	Thymus	Thymus
18	chr4:55523400-55524200	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:55523400-55524200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:55523400-55524400	Active TSS	Primary T cells from cord blood	blood
21	chr4:55523400-55524600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
22	chr4:55523400-55524600	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr4:55523400-55524600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
24	chr4:55523400-55524600	Flanking Active TSS	Pancreas	Pancrea
25	chr4:55523400-55524600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
26	chr4:55523400-55524600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
27	chr4:55523400-55524600	Bivalent/Poised TSS	NHLF	lung
28	chr4:55523400-55524800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
29	chr4:55523400-55524800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr4:55523400-55524800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
31	chr4:55523400-55525000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:55523400-55525400	Active TSS	Brain Angular Gyrus	brain
33	chr4:55523400-55525400	Active TSS	Brain Anterior Caudate	brain
34	chr4:55523400-55525400	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr4:55523400-55525400	Active TSS	Gastric	stomach
36	chr4:55523400-55525600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:55523400-55525600	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr4:55523400-55525800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
39	chr4:55523400-55525800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
40	chr4:55523400-55525800	Active TSS	Aorta	Aorta
41	chr4:55523400-55525800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
42	chr4:55523400-55525800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
43	chr4:55523400-55526000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr4:55523400-55526000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:55523400-55526200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:55523400-55526400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
47	chr4:55523600-55524000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:55523600-55524000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:55523600-55524000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
50	chr4:55523600-55524000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--

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