Variant report

Variant	rs487906
Chromosome Location	chr1:94478562-94478563
allele	C/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	TCF12	chr1:94478304-94478655	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr1:94478144-94479328	H1-hESC	embryonic stem cell:	n/a	chr1:94478426-94478435 chr1:94478426-94478435 chr1:94479090-94479099 chr1:94478427-94478434 chr1:94478234-94478244 chr1:94479090-94479099 chr1:94479091-94479098 chr1:94479089-94479099 chr1:94479089-94479099
3	USF1	chr1:94478229-94478700	H1-hESC	embryonic stem cell:	n/a	chr1:94478467-94478483
4	E2F6	chr1:94478010-94478617	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr1:94478312-94478729	H1-hESC	embryonic stem cell:	n/a	n/a
6	GATA1	chr1:94478033-94479283	PBDE	blood:	n/a	chr1:94478810-94478831 chr1:94478813-94478829 chr1:94478257-94478266 chr1:94478817-94478826 chr1:94478813-94478829
7	TCF12	chr1:94478222-94478684	H1-hESC	embryonic stem cell:	n/a	n/a
8	GTF2F1	chr1:94478401-94478640	H1-hESC	embryonic stem cell:	n/a	n/a
9	USF2	chr1:94478227-94478621	H1-hESC	embryonic stem cell:	n/a	chr1:94478467-94478483
10	MAX	chr1:94477644-94478690	H1-hESC	embryonic stem cell:	n/a	chr1:94478426-94478435 chr1:94478426-94478435 chr1:94478427-94478434 chr1:94478234-94478244
11	E2F6	chr1:94477037-94479451	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr1:94478133-94478611	HepG2	liver:	n/a	chr1:94478426-94478435 chr1:94478426-94478435 chr1:94478427-94478434 chr1:94478234-94478244
13	BHLHE40	chr1:94478253-94478593	HepG2	liver:	n/a	chr1:94478467-94478483
14	MAX	chr1:94478169-94478605	K562	blood:	n/a	chr1:94478426-94478435 chr1:94478426-94478435 chr1:94478427-94478434 chr1:94478234-94478244
15	MYC	chr1:94478070-94479282	K562	blood:	n/a	chr1:94478426-94478435 chr1:94478426-94478435 chr1:94479090-94479099 chr1:94478427-94478434 chr1:94478234-94478244 chr1:94479090-94479099 chr1:94479091-94479098 chr1:94479089-94479099 chr1:94479089-94479099
16	MAX	chr1:94478168-94478653	H1-hESC	embryonic stem cell:	n/a	chr1:94478426-94478435 chr1:94478426-94478435 chr1:94478427-94478434 chr1:94478234-94478244
17	FOXA1	chr1:94478154-94478571	HepG2	liver:	n/a	n/a
18	SIN3AK20	chr1:94478287-94478604	H1-hESC	embryonic stem cell:	n/a	n/a
19	HDAC2	chr1:94478200-94478582	H1-hESC	embryonic stem cell:	n/a	n/a
20	BHLHE40	chr1:94478242-94479148	K562	blood:	n/a	chr1:94478467-94478483
21	USF1	chr1:94478218-94478614	H1-hESC	embryonic stem cell:	n/a	chr1:94478467-94478483
22	MXI1	chr1:94478254-94478692	H1-hESC	embryonic stem cell:	n/a	chr1:94478514-94478529
23	SIN3A	chr1:94478157-94478717	H1-hESC	embryonic stem cell:	n/a	chr1:94478524-94478532
24	MAX	chr1:94478106-94478646	HepG2	liver:	n/a	chr1:94478426-94478435 chr1:94478426-94478435 chr1:94478427-94478434 chr1:94478234-94478244

Variant related genes	Relation type
ABCA4	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1191234	0.80[ASW][hapmap];0.82[GIH][hapmap];0.81[LWK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs17110714	1.00[CEU][hapmap]
rs3747961	1.00[CEU][hapmap]
rs557026	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs565155	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[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	nsv516137	chr1:94404238-94504545	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94471200-94480600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:94475400-94485600	Weak transcription	NH-A	brain
3	chr1:94476400-94479000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:94476400-94479200	Enhancers	Fetal Muscle Trunk	muscle
5	chr1:94476400-94479400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:94476400-94480000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:94476600-94479400	Enhancers	Placenta	Placenta
8	chr1:94476600-94479600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr1:94476800-94478600	Enhancers	Fetal Muscle Leg	muscle
10	chr1:94476800-94479200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:94476800-94480400	Enhancers	Fetal Intestine Large	intestine
12	chr1:94477000-94478600	Enhancers	Ovary	ovary
13	chr1:94477000-94479000	Enhancers	Right Atrium	heart
14	chr1:94477000-94479400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
15	chr1:94477000-94479800	Enhancers	Fetal Intestine Small	intestine
16	chr1:94477000-94481600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:94477200-94478600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
18	chr1:94477200-94479200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:94477200-94479200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:94477200-94480400	Weak transcription	HMEC	breast
21	chr1:94477400-94478600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:94477400-94478600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:94477400-94479800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr1:94477400-94480000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:94477400-94480200	Enhancers	Brain Germinal Matrix	brain
26	chr1:94477600-94478600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:94477600-94478600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
28	chr1:94477600-94478600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
29	chr1:94477600-94478800	Enhancers	Fetal Stomach	stomach
30	chr1:94477600-94479200	Enhancers	Duodenum Mucosa	Duodenum
31	chr1:94477600-94479200	Enhancers	HepG2	liver
32	chr1:94477600-94479400	Enhancers	H9 Cell Line	embryonic stem cell
33	chr1:94477600-94479400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
34	chr1:94477800-94479000	Weak transcription	HSMM	muscle
35	chr1:94477800-94479800	Weak transcription	Spleen	Spleen
36	chr1:94478000-94479600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
37	chr1:94478000-94479800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
38	chr1:94478200-94478600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:94478200-94479000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:94478200-94479200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:94478400-94479600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:94478400-94480000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
43	chr1:94478400-94480400	Weak transcription	Osteobl	bone

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