Variant report

Variant	rs10874835
Chromosome Location	chr1:94591481-94591482
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	CEBPB	chr1:94591475-94591752	HepG2	liver:	n/a	n/a
2	HDAC2	chr1:94591355-94591884	HepG2	liver:	n/a	n/a
3	USF1	chr1:94591259-94591826	ECC-1	luminal epithelium:	n/a	chr1:94591529-94591540
4	JUND	chr1:94591384-94591888	HepG2	liver:	n/a	n/a
5	USF1	chr1:94591356-94591718	H1-hESC	embryonic stem cell:	n/a	chr1:94591529-94591540
6	CEBPB	chr1:94591165-94591692	A549	lung:	n/a	chr1:94591311-94591320 chr1:94591257-94591266 chr1:94591311-94591320 chr1:94591311-94591320
7	USF1	chr1:94591355-94591653	A549	lung:	n/a	chr1:94591529-94591540
8	SMC3	chr1:94591280-94592114	HepG2	liver:	n/a	n/a
9	HDAC2	chr1:94591342-94592123	HepG2	liver:	n/a	n/a
10	USF2	chr1:94591329-94591992	HepG2	liver:	n/a	chr1:94591529-94591540
11	CEBPB	chr1:94591405-94591827	HepG2	liver:	n/a	n/a
12	USF1	chr1:94591342-94591708	HepG2	liver:	n/a	chr1:94591529-94591540
13	FOS	chr1:94591170-94591534	MCF10A-Er-Src	breast:	n/a	n/a
14	USF1	chr1:94591381-94591594	SK-N-SH_RA	brain:	n/a	chr1:94591529-94591540
15	CEBPZ	chr1:94591401-94591676	HepG2	liver:	n/a	n/a
16	USF1	chr1:94591357-94591757	ECC-1	luminal epithelium:	n/a	chr1:94591529-94591540
17	USF1	chr1:94591450-94591638	A549	lung:	n/a	chr1:94591529-94591540
18	USF1	chr1:94591351-94591669	H1-hESC	embryonic stem cell:	n/a	chr1:94591529-94591540
19	CEBPB	chr1:94591363-94591854	HepG2	liver:	n/a	n/a
20	MYBL2	chr1:94591272-94592055	HepG2	liver:	n/a	n/a
21	HEY1	chr1:94591241-94591570	HepG2	liver:	n/a	n/a
22	MAX	chr1:94591267-94592160	HepG2	liver:	n/a	chr1:94591531-94591540
23	TEAD4	chr1:94591290-94592234	HepG2	liver:	n/a	n/a
24	FOXA2	chr1:94591199-94592092	HepG2	liver:	n/a	n/a
25	MAFK	chr1:94591283-94591846	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:94591383-94591515	HepG2	liver:	n/a	n/a
27	FOXA2	chr1:94591292-94592017	HepG2	liver:	n/a	n/a
28	RXRA	chr1:94591341-94591948	HepG2	liver:	n/a	n/a
29	RCOR1	chr1:94591425-94591750	HepG2	liver:	n/a	n/a
30	HNF4G	chr1:94591343-94591985	HepG2	liver:	n/a	n/a
31	ARID3A	chr1:94591083-94592179	HepG2	liver:	n/a	n/a
32	MAX	chr1:94591393-94591812	HepG2	liver:	n/a	chr1:94591531-94591540
33	MXI1	chr1:94591373-94592060	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:94591323-94591578	HepG2	liver:	n/a	n/a
35	EP300	chr1:94591354-94591964	HepG2	liver:	n/a	n/a
36	MAFK	chr1:94591401-94591613	HepG2	liver:	n/a	n/a
37	CEBPB	chr1:94591162-94591482	Hela-S3	cervix:	n/a	chr1:94591311-94591320 chr1:94591257-94591266 chr1:94591311-94591320 chr1:94591311-94591320
38	NFIC	chr1:94591426-94591966	HepG2	liver:	n/a	n/a
39	REST	chr1:94591289-94591800	HepG2	liver:	n/a	n/a
40	BRCA1	chr1:94591448-94591557	HepG2	liver:	n/a	n/a
41	EP300	chr1:94591311-94591924	HepG2	liver:	n/a	n/a
42	CEBPB	chr1:94591132-94591851	HepG2	liver:	n/a	chr1:94591311-94591320 chr1:94591257-94591266 chr1:94591311-94591320 chr1:94591311-94591320
43	USF1	chr1:94591362-94591637	A549	lung:	n/a	chr1:94591529-94591540
44	TBP	chr1:94591327-94592029	HepG2	liver:	n/a	n/a
45	CEBPB	chr1:94591070-94591576	ECC-1	luminal epithelium:	n/a	chr1:94591311-94591320 chr1:94591257-94591266 chr1:94591311-94591320 chr1:94591311-94591320
46	CEBPB	chr1:94591024-94591600	A549	lung:	n/a	chr1:94591311-94591320 chr1:94591257-94591266 chr1:94591311-94591320 chr1:94591311-94591320
47	HEY1	chr1:94591292-94592040	HepG2	liver:	n/a	n/a
48	MBD4	chr1:94591208-94592051	HepG2	liver:	n/a	n/a
49	MAFF	chr1:94591463-94591966	HepG2	liver:	n/a	n/a
50	USF1	chr1:94591346-94591714	HepG2	liver:	n/a	chr1:94591529-94591540

Variant related genes	Relation type
ABCA4	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10493869	0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10493870	0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11165076	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165079	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165080	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165082	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11588391	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12025221	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12035820	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17111122	0.86[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs1931564	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1931566	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1931570	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789439	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3789440	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3789442	0.86[CHD][hapmap];0.83[JPT][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3789443	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3789444	0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3789445	0.89[TSI][hapmap]
rs3827714	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4147798	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4147801	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61784007	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61784009	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][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	nsv871416	chr1:94566311-94635028	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv870932	chr1:94579053-94607607	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv871679	chr1:94579426-94598568	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv871502	chr1:94579426-94607607	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv871306	chr1:94579426-94609478	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv871210	chr1:94579426-94629643	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv523430	chr1:94582249-94591481	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10874835	FAM69A	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94564600-94591800	Weak transcription	Right Atrium	heart
2	chr1:94586200-94591600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:94586200-94591600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:94586200-94591800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:94587000-94592400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:94587400-94591600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:94587600-94591600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:94587600-94591600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:94587600-94591600	Enhancers	HepG2	liver
10	chr1:94588600-94595000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:94588600-94596400	Weak transcription	Osteobl	bone
12	chr1:94588600-94596600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:94590600-94591800	Weak transcription	HUVEC	blood vessel
14	chr1:94590800-94592200	Enhancers	A549	lung
15	chr1:94591400-94591600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:94591400-94591600	Flanking Bivalent TSS/Enh	Pancreas	Pancrea
17	chr1:94591400-94591600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
18	chr1:94591400-94591800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr1:94591400-94592000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:94591400-94592000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:94591400-94592000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:94591400-94592000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr1:94591400-94592000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:94591400-94592000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:94591400-94592000	Enhancers	Fetal Muscle Leg	muscle
26	chr1:94591400-94592000	Enhancers	Placenta	Placenta
27	chr1:94591400-94592000	Enhancers	Left Ventricle	heart
28	chr1:94591400-94592000	Enhancers	Placenta Amnion	Placenta Amnion
29	chr1:94591400-94592200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr1:94591400-94592200	Enhancers	Liver	Liver
31	chr1:94591400-94592200	Enhancers	Fetal Kidney	kidney
32	chr1:94591400-94592400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr1:94591400-94592400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:94591400-94592400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:94591400-94592400	Enhancers	Adipose Nuclei	Adipose

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