Variant report

Variant	rs28706082
Chromosome Location	chr1:85100640-85100641
allele	C/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	GATA3	chr1:85100176-85100901	T-47D	breast:	n/a	n/a
2	SRF	chr1:85100216-85100970	MCF-7	breast:	n/a	n/a
3	ESR1	chr1:85100447-85100800	T-47D	breast:	n/a	n/a
4	TCF7L2	chr1:85100002-85101261	MCF-7	breast:	n/a	chr1:85100804-85100818 chr1:85101208-85101218
5	NR2F2	chr1:85099956-85101008	MCF-7	breast:	n/a	n/a
6	FOSL2	chr1:85100321-85100839	MCF-7	breast:	n/a	n/a
7	NR2F2	chr1:85100036-85100951	MCF-7	breast:	n/a	n/a
8	MYC	chr1:85100419-85100797	MCF10A-Er-Src	breast:	n/a	n/a
9	MAFK	chr1:85100587-85100922	IMR90	lung:	n/a	chr1:85100750-85100765
10	CEBPB	chr1:85100236-85100883	MCF-7	breast:	n/a	n/a
11	FOXA1	chr1:85100344-85100729	T-47D	breast:	n/a	n/a
12	MYC	chr1:85100504-85100724	MCF-7	breast:	n/a	n/a
13	GATA3	chr1:85100157-85100817	T-47D	breast:	n/a	n/a
14	EP300	chr1:85100406-85100815	T-47D	breast:	n/a	n/a
15	SIN3AK20	chr1:85100060-85100977	MCF-7	breast:	n/a	n/a
16	ESR1	chr1:85100347-85100799	T-47D	breast:	n/a	n/a
17	STAT3	chr1:85100251-85100791	MCF10A-Er-Src	breast:	n/a	n/a
18	MAFK	chr1:85100586-85100939	HepG2	liver:	n/a	chr1:85100750-85100765
19	CEBPB	chr1:85100185-85100791	MCF-7	breast:	n/a	n/a
20	TCF7L2	chr1:85100594-85101140	HEK293	kidney:	n/a	chr1:85100804-85100818
21	MAFK	chr1:85100581-85100945	HepG2	liver:	n/a	chr1:85100750-85100765
22	HDAC2	chr1:85100186-85100860	MCF-7	breast:	n/a	n/a
23	GATA3	chr1:85100221-85100871	MCF-7	breast:	n/a	n/a
24	FOS	chr1:85100341-85100878	MCF10A-Er-Src	breast:	n/a	chr1:85100858-85100867
25	ZNF217	chr1:85100197-85101075	MCF-7	breast:	n/a	n/a
26	FOS	chr1:85100487-85100748	MCF10A-Er-Src	breast:	n/a	n/a
27	GATA3	chr1:85099944-85101091	MCF-7	breast:	n/a	n/a
28	FOS	chr1:85100315-85100816	MCF10A-Er-Src	breast:	n/a	n/a
29	GATA3	chr1:85100219-85100918	MCF-7	breast:	n/a	n/a
30	SIN3AK20	chr1:85099921-85101168	MCF-7	breast:	n/a	n/a
31	MAFF	chr1:85100585-85100894	K562	blood:	n/a	chr1:85100748-85100766
32	MAFK	chr1:85100620-85100925	H1-hESC	embryonic stem cell:	n/a	chr1:85100750-85100765
33	STAT3	chr1:85100314-85100791	MCF10A-Er-Src	breast:	n/a	n/a
34	HDAC2	chr1:85100208-85100991	MCF-7	breast:	n/a	n/a
35	TEAD4	chr1:85100354-85100879	MCF-7	breast:	n/a	n/a
36	MAFK	chr1:85100604-85100919	K562	blood:	n/a	chr1:85100750-85100765
37	FOXM1	chr1:85100179-85101040	MCF-7	breast:	n/a	n/a
38	EP300	chr1:85100161-85100918	MCF-7	breast:	n/a	n/a
39	EP300	chr1:85100372-85100766	T-47D	breast:	n/a	n/a
40	GATA3	chr1:85099995-85100997	MCF-7	breast:	n/a	n/a
41	MAX	chr1:85100286-85100845	MCF-7	breast:	n/a	n/a
42	MYC	chr1:85100622-85100678	MCF-7	breast:	n/a	n/a
43	MAFF	chr1:85100580-85100934	HepG2	liver:	n/a	chr1:85100748-85100766

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85094796..85097662-chr1:85099991..85101818,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf180-2	chr1:85100615-85100703	NR_027379

Variant related genes	Relation type
C1orf180	TF binding region
ENSG00000180869	Chromatin interaction

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

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

rs_ID	r²[population]
rs11163998	1.00[EUR][1000 genomes]
rs11164002	1.00[EUR][1000 genomes]
rs11164013	1.00[EUR][1000 genomes]
rs11164022	1.00[EUR][1000 genomes]
rs11164024	1.00[EUR][1000 genomes]
rs11164025	1.00[EUR][1000 genomes]
rs11807815	1.00[EUR][1000 genomes]
rs12058889	1.00[EUR][1000 genomes]
rs12058978	1.00[EUR][1000 genomes]
rs12059657	1.00[EUR][1000 genomes]
rs12062111	1.00[AMR][1000 genomes]
rs12068340	1.00[EUR][1000 genomes]
rs12070049	1.00[EUR][1000 genomes]
rs12075688	1.00[EUR][1000 genomes]
rs12076236	1.00[EUR][1000 genomes]
rs12077315	1.00[EUR][1000 genomes]
rs12080425	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084716	1.00[EUR][1000 genomes]
rs12091312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12092806	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12093770	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12095492	1.00[EUR][1000 genomes]
rs12095537	1.00[EUR][1000 genomes]
rs12096153	1.00[EUR][1000 genomes]
rs12097619	1.00[EUR][1000 genomes]
rs1591972	1.00[EUR][1000 genomes]
rs1803276	1.00[EUR][1000 genomes]
rs28667025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2945131	1.00[EUR][1000 genomes]
rs2945132	1.00[EUR][1000 genomes]
rs2994926	1.00[EUR][1000 genomes]
rs2994927	1.00[EUR][1000 genomes]
rs59323332	1.00[AMR][1000 genomes]
rs60192023	1.00[AMR][1000 genomes]
rs6665333	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6669324	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950312	1.00[EUR][1000 genomes]
rs74096103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74098423	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74098426	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74098430	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74098433	1.00[AMR][1000 genomes]
rs74098441	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74098442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74098443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74098453	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74098454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7517977	1.00[AMR][1000 genomes]
rs7532040	1.00[EUR][1000 genomes]
rs7544392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9661833	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	nsv1000325	chr1:85032605-85100748	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85087000-85147400	Weak transcription	Gastric	stomach
2	chr1:85096400-85101600	Enhancers	Fetal Intestine Large	intestine
3	chr1:85096400-85101600	Enhancers	Fetal Intestine Small	intestine
4	chr1:85097200-85101200	Enhancers	Duodenum Mucosa	Duodenum
5	chr1:85098000-85101400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:85098000-85101400	Enhancers	NHEK	skin
7	chr1:85098000-85101600	Enhancers	Placenta	Placenta
8	chr1:85098000-85101600	Enhancers	HMEC	breast
9	chr1:85098400-85101400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:85098400-85101800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:85099000-85109600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:85099000-85115600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:85099000-85123400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:85099200-85109200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:85099200-85109800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:85099200-85115000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:85099200-85121400	Weak transcription	NHDF-Ad	bronchial
18	chr1:85099200-85138200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:85099400-85105600	Weak transcription	K562	blood
20	chr1:85099400-85115000	Weak transcription	Osteobl	bone
21	chr1:85099400-85131200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:85099600-85122600	Weak transcription	Fetal Brain Male	brain
23	chr1:85099800-85101000	Enhancers	Hela-S3	cervix
24	chr1:85100000-85100800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:85100000-85101000	Enhancers	Fetal Kidney	kidney
26	chr1:85100200-85100800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr1:85100200-85106200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:85100400-85101000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:85100600-85101000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:85100600-85101000	Enhancers	Esophagus	oesophagus
31	chr1:85100600-85101200	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr1:85100600-85112400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:85100600-85116800	Weak transcription	Rectal Mucosa Donor 29	rectum

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