Variant report

Variant	rs12085639
Chromosome Location	chr1:94478293-94478294
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	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
2	MAX	chr1:94478244-94478501	HepG2	liver:	n/a	chr1:94478426-94478435 chr1:94478426-94478435 chr1:94478427-94478434
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	GATA1	chr1:94478033-94479283	PBDE	blood:	n/a	chr1:94478810-94478831 chr1:94478813-94478829 chr1:94478257-94478266 chr1:94478817-94478826 chr1:94478813-94478829
6	TCF12	chr1:94478222-94478684	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr1:94478246-94478530	H1-hESC	embryonic stem cell:	n/a	n/a
8	USF2	chr1:94478227-94478621	H1-hESC	embryonic stem cell:	n/a	chr1:94478467-94478483
9	MAX	chr1:94477644-94478690	H1-hESC	embryonic stem cell:	n/a	chr1:94478426-94478435 chr1:94478426-94478435 chr1:94478427-94478434 chr1:94478234-94478244
10	MAZ	chr1:94478202-94478406	K562	blood:	n/a	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	MYC	chr1:94478224-94478522	H1-hESC	embryonic stem cell:	n/a	chr1:94478426-94478435 chr1:94478426-94478435 chr1:94478427-94478434 chr1:94478234-94478244
20	HDAC2	chr1:94478200-94478582	H1-hESC	embryonic stem cell:	n/a	n/a
21	BHLHE40	chr1:94478242-94479148	K562	blood:	n/a	chr1:94478467-94478483
22	USF1	chr1:94478218-94478614	H1-hESC	embryonic stem cell:	n/a	chr1:94478467-94478483
23	JUND	chr1:94478252-94478380	K562	blood:	n/a	n/a
24	MXI1	chr1:94478254-94478692	H1-hESC	embryonic stem cell:	n/a	chr1:94478514-94478529
25	SIN3A	chr1:94478157-94478717	H1-hESC	embryonic stem cell:	n/a	chr1:94478524-94478532
26	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]
rs12082181	0.87[CHD][hapmap]
rs17391542	0.88[TSI][hapmap]
rs4147853	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58088273	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs945067	0.84[MEX][hapmap]

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:45 , 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	chr1:94477400-94478400	Enhancers	Osteobl	bone
22	chr1:94477400-94478600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:94477400-94478600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr1:94477400-94479800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
25	chr1:94477400-94480000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:94477400-94480200	Enhancers	Brain Germinal Matrix	brain
27	chr1:94477600-94478600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:94477600-94478600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
29	chr1:94477600-94478600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
30	chr1:94477600-94478800	Enhancers	Fetal Stomach	stomach
31	chr1:94477600-94479200	Enhancers	Duodenum Mucosa	Duodenum
32	chr1:94477600-94479200	Enhancers	HepG2	liver
33	chr1:94477600-94479400	Enhancers	H9 Cell Line	embryonic stem cell
34	chr1:94477600-94479400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
35	chr1:94477800-94479000	Weak transcription	HSMM	muscle
36	chr1:94477800-94479800	Weak transcription	Spleen	Spleen
37	chr1:94478000-94479600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
38	chr1:94478000-94479800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
39	chr1:94478200-94478400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:94478200-94478400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
41	chr1:94478200-94478400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:94478200-94478400	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr1:94478200-94478600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:94478200-94479000	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr1:94478200-94479200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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