Variant report

Variant	rs236326
Chromosome Location	chr1:94057720-94057721
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	MAX	chr1:94057163-94058270	ECC-1	luminal epithelium:	n/a	chr1:94057611-94057621
2	TCF12	chr1:94057191-94057797	HepG2	liver:	n/a	chr1:94057476-94057483 chr1:94057400-94057410
3	TAF1	chr1:94057318-94058091	HepG2	liver:	n/a	n/a
4	USF1	chr1:94057294-94057854	HepG2	liver:	n/a	n/a
5	ATF2	chr1:94057189-94057888	GM12878	blood:	n/a	n/a
6	MYBL2	chr1:94056892-94058052	HepG2	liver:	n/a	n/a
7	FOXA1	chr1:94056892-94057867	HepG2	liver:	n/a	chr1:94057695-94057707
8	POLR2A	chr1:94057137-94058481	PFSK-1	brain:	n/a	n/a
9	SIN3AK20	chr1:94057241-94057721	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr1:94057321-94057741	GM12891	blood:	n/a	n/a
11	NFATC1	chr1:94057307-94057783	GM12878	blood:	n/a	n/a
12	MBD4	chr1:94057120-94058544	HepG2	liver:	n/a	n/a
13	RUNX3	chr1:94057140-94057854	GM12878	blood:	n/a	n/a
14	EP300	chr1:94056874-94057981	HepG2	liver:	n/a	chr1:94057621-94057631 chr1:94057084-94057097
15	FOXA1	chr1:94056858-94057998	HepG2	liver:	n/a	chr1:94057695-94057707
16	NFIC	chr1:94057137-94057863	ECC-1	luminal epithelium:	n/a	chr1:94057471-94057488 chr1:94057472-94057488
17	FOXA2	chr1:94057212-94057850	HepG2	liver:	n/a	chr1:94057695-94057707
18	CEBPB	chr1:94056909-94057760	HepG2	liver:	n/a	n/a
19	POLR2A	chr1:94057236-94058879	HepG2	liver:	n/a	n/a
20	MEF2A	chr1:94057309-94057820	GM12878	blood:	n/a	chr1:94057682-94057697 chr1:94057682-94057697
21	POLR2A	chr1:94057671-94058392	Hela-S3	cervix:	n/a	n/a
22	REST	chr1:94057220-94058152	HepG2	liver:	n/a	n/a
23	TBP	chr1:94057166-94058528	HepG2	liver:	n/a	n/a
24	FOSL2	chr1:94057218-94057943	HepG2	liver:	n/a	n/a
25	YY1	chr1:94057220-94058091	HepG2	liver:	n/a	n/a
26	MAX	chr1:94057250-94057734	K562	blood:	n/a	chr1:94057611-94057621
27	MYC	chr1:94056936-94057768	NB4	blood:	n/a	chr1:94057611-94057621
28	MTA3	chr1:94057232-94057834	GM12878	blood:	n/a	n/a
29	BATF	chr1:94057304-94057732	GM12878	blood:	n/a	n/a
30	MXI1	chr1:94057018-94057935	SK-N-SH	brain:	n/a	chr1:94057400-94057409
31	POU2F2	chr1:94057329-94057843	GM12891	blood:	n/a	chr1:94057407-94057419
32	HEY1	chr1:94056860-94058945	HepG2	liver:	n/a	n/a
33	FOXA1	chr1:94056868-94057858	HepG2	liver:	n/a	chr1:94057695-94057707
34	BCLAF1	chr1:94057324-94057782	GM12878	blood:	n/a	n/a
35	HNF4G	chr1:94057335-94057724	HepG2	liver:	n/a	n/a
36	ATF2	chr1:94057328-94057824	GM12878	blood:	n/a	n/a
37	MYBL2	chr1:94056859-94058226	HepG2	liver:	n/a	n/a
38	ELF1	chr1:94057360-94057861	GM12878	blood:	n/a	chr1:94057522-94057535
39	RCOR1	chr1:94057193-94058084	HepG2	liver:	n/a	n/a
40	ELF1	chr1:94056907-94057923	HepG2	liver:	n/a	chr1:94057522-94057535
41	NFIC	chr1:94057102-94058256	ECC-1	luminal epithelium:	n/a	chr1:94057471-94057488 chr1:94057472-94057488
42	JUND	chr1:94057410-94057864	HepG2	liver:	n/a	n/a
43	POLR2A	chr1:94057281-94058420	HepG2	liver:	n/a	n/a
44	USF2	chr1:94057616-94057909	HepG2	liver:	n/a	n/a
45	ELF1	chr1:94057332-94057855	HepG2	liver:	n/a	chr1:94057522-94057535
46	MYC	chr1:94057312-94058054	HepG2	liver:	n/a	chr1:94057611-94057621
47	HDAC2	chr1:94057267-94057923	HepG2	liver:	n/a	n/a
48	HNF4A	chr1:94057249-94057894	HepG2	liver:	n/a	n/a
49	RELA	chr1:94057059-94057829	GM19099	blood:	n/a	n/a
50	FOXM1	chr1:94057155-94057870	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FNBP1L-1	chr1:94057719-94057754	NONHSAT004536
2	lnc-FNBP1L-1	chr1:94057525-94058065	NONHSAT004537

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

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs17110124	0.98[ASN][1000 genomes]
rs2281474	0.91[ASN][1000 genomes]
rs236321	0.91[EUR][1000 genomes]
rs236322	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236323	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236329	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236330	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236331	0.95[ASN][1000 genomes]
rs236332	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236333	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236335	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3767973	0.89[ASN][1000 genomes]
rs3767975	0.88[ASN][1000 genomes]
rs3767976	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767977	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57012808	0.91[ASN][1000 genomes]
rs57466479	0.89[ASN][1000 genomes]
rs57914444	0.89[ASN][1000 genomes]
rs59777284	0.89[ASN][1000 genomes]
rs6661488	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671749	0.95[ASN][1000 genomes]
rs6692801	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516400	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518795	0.94[ASN][1000 genomes]
rs7519939	0.95[ASN][1000 genomes]
rs7524368	0.89[ASN][1000 genomes]
rs7551964	0.95[ASN][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:106 , 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	chr1:94053000-94058000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:94053000-94058000	Strong transcription	NHEK	skin
16	chr1:94053200-94058200	Strong transcription	NHDF-Ad	bronchial
17	chr1:94053600-94058000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:94053600-94058000	Weak transcription	Right Atrium	heart
19	chr1:94053600-94063000	Genic enhancers	Muscle Satellite Cultured Cells	--
20	chr1:94054200-94058200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:94054200-94058400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:94054400-94061000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:94054600-94058400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr1:94054600-94062000	Weak transcription	Brain Substantia Nigra	brain
25	chr1:94055000-94058200	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:94055000-94059200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:94055200-94058800	Enhancers	Primary hematopoietic stem cells	blood
28	chr1:94055400-94057800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:94055400-94057800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:94055600-94057800	Weak transcription	Brain Anterior Caudate	brain
31	chr1:94055600-94058800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:94055800-94057800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:94055800-94058000	Weak transcription	HSMMtube	muscle
34	chr1:94055800-94058200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:94055800-94061000	Weak transcription	Aorta	Aorta
36	chr1:94056000-94057800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr1:94056000-94066000	Weak transcription	Ovary	ovary
38	chr1:94056200-94058000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:94056400-94057800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:94056400-94058000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:94056800-94057800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr1:94056800-94058000	Enhancers	Fetal Thymus	thymus
43	chr1:94056800-94058200	Enhancers	Primary B cells from peripheral blood	blood
44	chr1:94056800-94060200	Enhancers	Pancreas	Pancrea
45	chr1:94057000-94057800	Enhancers	Thymus	Thymus
46	chr1:94057000-94057800	Enhancers	K562	blood
47	chr1:94057000-94057800	Genic enhancers	Osteobl	bone
48	chr1:94057000-94058000	Genic enhancers	Fetal Muscle Leg	muscle
49	chr1:94057000-94058200	Transcr. at gene 5' and 3'	A549	lung
50	chr1:94057000-94058400	Flanking Active TSS	Liver	Liver

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