Variant report

Variant	rs236325
Chromosome Location	chr1:94057048-94057049
allele	A/T
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	FOXA2	chr1:94056977-94057202	HepG2	liver:	n/a	n/a
2	MYBL2	chr1:94056892-94058052	HepG2	liver:	n/a	n/a
3	FOXA1	chr1:94056892-94057867	HepG2	liver:	n/a	chr1:94057695-94057707
4	TCF12	chr1:94056879-94057428	A549	lung:	n/a	chr1:94057400-94057410
5	EP300	chr1:94056874-94057981	HepG2	liver:	n/a	chr1:94057621-94057631 chr1:94057084-94057097
6	FOXA1	chr1:94056858-94057998	HepG2	liver:	n/a	chr1:94057695-94057707
7	CEBPB	chr1:94056909-94057760	HepG2	liver:	n/a	n/a
8	MYC	chr1:94056936-94057768	NB4	blood:	n/a	chr1:94057611-94057621
9	EBF1	chr1:94057035-94057642	GM12878	blood:	n/a	chr1:94057145-94057154 chr1:94057145-94057155
10	CHD2	chr1:94057025-94057477	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:94056816-94057112	HepG2	liver:	n/a	n/a
12	MXI1	chr1:94057018-94057935	SK-N-SH	brain:	n/a	chr1:94057400-94057409
13	HEY1	chr1:94056860-94058945	HepG2	liver:	n/a	n/a
14	FOXA1	chr1:94056868-94057858	HepG2	liver:	n/a	chr1:94057695-94057707
15	CEBPB	chr1:94056925-94057168	A549	lung:	n/a	n/a
16	EP300	chr1:94057047-94057151	GM12878	blood:	n/a	chr1:94057084-94057097
17	MYBL2	chr1:94056859-94058226	HepG2	liver:	n/a	n/a
18	ELF1	chr1:94056907-94057923	HepG2	liver:	n/a	chr1:94057522-94057535
19	SPI1	chr1:94056885-94057464	HL-60	blood:	n/a	chr1:94057292-94057305
20	POLR2A	chr1:94057002-94057957	PFSK-1	brain:	n/a	n/a
21	MAX	chr1:94056989-94057809	NB4	blood:	n/a	chr1:94057611-94057621
22	SP1	chr1:94056917-94057306	A549	lung:	n/a	chr1:94057062-94057076
23	SP1	chr1:94056830-94057945	HepG2	liver:	n/a	chr1:94057062-94057076
24	FOXA2	chr1:94056838-94057512	A549	lung:	n/a	n/a
25	NFIC	chr1:94057013-94057850	SK-N-SH	brain:	n/a	chr1:94057471-94057488 chr1:94057472-94057488
26	TEAD4	chr1:94057010-94057893	HepG2	liver:	n/a	n/a
27	EP300	chr1:94056938-94057954	HepG2	liver:	n/a	chr1:94057621-94057631 chr1:94057084-94057097
28	MAX	chr1:94056964-94059251	HepG2	liver:	n/a	chr1:94057611-94057621
29	ELF1	chr1:94056918-94057245	HepG2	liver:	n/a	n/a
30	REST	chr1:94056937-94057760	PFSK-1	brain:	n/a	chr1:94057103-94057112
31	ZNF384	chr1:94056891-94057497	GM12878	blood:	n/a	n/a
32	FOXA1	chr1:94056879-94057991	HepG2	liver:	n/a	chr1:94057695-94057707
33	MAX	chr1:94057000-94058505	HepG2	liver:	n/a	chr1:94057611-94057621
34	NFIC	chr1:94056919-94057988	HepG2	liver:	n/a	chr1:94057471-94057488 chr1:94057472-94057488
35	NFIC	chr1:94056941-94058131	HepG2	liver:	n/a	chr1:94057471-94057488 chr1:94057472-94057488
36	ARID3A	chr1:94056947-94057872	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000224093	TF binding region
BCAR3	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11164950	1.00[EUR][1000 genomes]
rs171030	1.00[AMR][1000 genomes]
rs1772780	1.00[AMR][1000 genomes]
rs180499	1.00[AMR][1000 genomes]
rs183539	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1863500	1.00[EUR][1000 genomes]
rs236264	1.00[AMR][1000 genomes]
rs236269	1.00[AMR][1000 genomes]
rs236272	1.00[AMR][1000 genomes]
rs236276	1.00[AMR][1000 genomes]
rs236279	1.00[AMR][1000 genomes]
rs236282	1.00[AMR][1000 genomes]
rs236286	1.00[AMR][1000 genomes]
rs236289	1.00[AMR][1000 genomes]
rs236290	1.00[AMR][1000 genomes]
rs236294	1.00[AMR][1000 genomes]
rs236297	1.00[AMR][1000 genomes]
rs236298	1.00[AMR][1000 genomes]
rs236299	1.00[AMR][1000 genomes]
rs236314	1.00[AMR][1000 genomes]
rs236324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs236327	1.00[EUR][1000 genomes]
rs236328	1.00[EUR][1000 genomes]
rs236334	1.00[EUR][1000 genomes]
rs236337	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs236338	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs236340	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs237424	1.00[EUR][1000 genomes]
rs237426	1.00[EUR][1000 genomes]
rs237427	1.00[EUR][1000 genomes]
rs237428	1.00[EUR][1000 genomes]
rs237429	1.00[EUR][1000 genomes]
rs237430	1.00[EUR][1000 genomes]
rs2449377	1.00[EUR][1000 genomes]
rs2493642	1.00[EUR][1000 genomes]
rs2818968	1.00[EUR][1000 genomes]
rs57438388	1.00[EUR][1000 genomes]
rs57974365	1.00[EUR][1000 genomes]
rs58430978	1.00[EUR][1000 genomes]
rs59039419	1.00[EUR][1000 genomes]
rs60515224	1.00[EUR][1000 genomes]
rs60717381	1.00[EUR][1000 genomes]
rs72961357	1.00[EUR][1000 genomes]
rs72961366	1.00[EUR][1000 genomes]
rs72961373	1.00[EUR][1000 genomes]
rs72961379	1.00[EUR][1000 genomes]
rs72961386	1.00[EUR][1000 genomes]
rs72961389	1.00[EUR][1000 genomes]
rs7547495	1.00[EUR][1000 genomes]
rs7553492	1.00[EUR][1000 genomes]
rs7554661	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94025600-94073800	Weak transcription	Fetal Brain Female	brain
2	chr1:94041800-94059400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:94042200-94063200	Weak transcription	Brain Germinal Matrix	brain
4	chr1:94043000-94058400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:94046600-94058200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:94048200-94059200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:94048200-94059400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:94048400-94059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:94048600-94064200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:94049600-94059400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:94050000-94059400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:94050800-94057800	Weak transcription	Small Intestine	intestine
13	chr1:94050800-94059200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:94051200-94057200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:94051200-94057200	Weak transcription	Fetal Kidney	kidney
16	chr1:94051400-94057600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:94052000-94057400	Weak transcription	Colonic Mucosa	Colon
18	chr1:94052400-94057600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:94053000-94058000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:94053000-94058000	Strong transcription	NHEK	skin
21	chr1:94053200-94058200	Strong transcription	NHDF-Ad	bronchial
22	chr1:94053400-94057600	Strong transcription	Stomach Smooth Muscle	stomach
23	chr1:94053600-94058000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:94053600-94058000	Weak transcription	Right Atrium	heart
25	chr1:94053600-94063000	Genic enhancers	Muscle Satellite Cultured Cells	--
26	chr1:94054200-94057200	Strong transcription	Placenta	Placenta
27	chr1:94054200-94057400	Strong transcription	Hela-S3	cervix
28	chr1:94054200-94058200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:94054200-94058400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:94054400-94061000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:94054600-94057200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:94054600-94057600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:94054600-94058400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr1:94054600-94062000	Weak transcription	Brain Substantia Nigra	brain
35	chr1:94054800-94057200	Weak transcription	Esophagus	oesophagus
36	chr1:94054800-94057200	Weak transcription	Psoas Muscle	Psoas
37	chr1:94054800-94057200	Weak transcription	Spleen	Spleen
38	chr1:94054800-94057400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:94055000-94057200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:94055000-94057200	Strong transcription	Adipose Nuclei	Adipose
41	chr1:94055000-94057200	Weak transcription	Right Ventricle	heart
42	chr1:94055000-94057200	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:94055000-94057400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:94055000-94057400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:94055000-94057400	Weak transcription	Gastric	stomach
46	chr1:94055000-94057600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:94055000-94058200	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:94055000-94059200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:94055200-94057200	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr1:94055200-94057400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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