Variant report

Variant	rs233074
Chromosome Location	chr1:85809065-85809066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85808320..85810414-chr1:86046436..86048176,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11161607	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161610	0.82[ASN][1000 genomes]
rs11161611	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12044537	0.80[EUR][1000 genomes]
rs12047422	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12124170	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125557	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12140103	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498373	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1498375	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1554597	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs173026	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs18582	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1884139	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2011825	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2012683	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2177461	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2207368	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2268667	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2300634	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2300637	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233047	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233050	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs233053	0.80[EUR][1000 genomes]
rs233054	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233055	0.82[EUR][1000 genomes]
rs233057	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233058	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233059	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233060	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233061	0.85[EUR][1000 genomes]
rs233062	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233066	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233067	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233068	0.87[EUR][1000 genomes]
rs233069	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233071	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233072	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs233091	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233093	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233095	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233097	0.87[EUR][1000 genomes]
rs233099	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233108	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233109	0.86[EUR][1000 genomes]
rs233112	0.86[EUR][1000 genomes]
rs233113	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233114	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233115	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233118	0.85[EUR][1000 genomes]
rs233119	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233120	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233121	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233124	0.85[EUR][1000 genomes]
rs233127	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233130	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233131	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233132	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233133	0.85[EUR][1000 genomes]
rs2892888	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3087894	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3768227	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3949301	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs423105	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949890	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949900	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6576764	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6576767	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6657817	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6671599	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66811655	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704103	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67611930	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72724606	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs761601	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs997251	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85796600-85809400	Weak transcription	Stomach Mucosa	stomach
2	chr1:85796800-85809600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:85798800-85824800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:85798800-85824800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:85799000-85813600	Weak transcription	Fetal Intestine Large	intestine
6	chr1:85800400-85815000	Weak transcription	Fetal Intestine Small	intestine
7	chr1:85804800-85811000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr1:85805800-85811400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:85806000-85810400	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr1:85806400-85815800	Weak transcription	Pancreas	Pancrea
11	chr1:85806600-85813600	Weak transcription	Left Ventricle	heart
12	chr1:85806600-85814200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:85806800-85810200	Weak transcription	Lung	lung
14	chr1:85807400-85809400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:85807400-85811000	Enhancers	NH-A	brain
16	chr1:85807600-85809200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr1:85807600-85809600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:85807600-85810000	Enhancers	HSMMtube	muscle
19	chr1:85807600-85810200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:85807600-85810600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr1:85807600-85810600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:85807600-85811000	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr1:85807600-85811200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr1:85807600-85812200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:85807600-85813400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:85807800-85809600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:85807800-85810000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr1:85807800-85810200	Enhancers	NHLF	lung
29	chr1:85807800-85810600	Enhancers	HMEC	breast
30	chr1:85807800-85811000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:85807800-85811600	Enhancers	Osteobl	bone
32	chr1:85808000-85809800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:85808000-85809800	Enhancers	Rectal Smooth Muscle	rectum
34	chr1:85808000-85810400	Enhancers	NHDF-Ad	bronchial
35	chr1:85808000-85810600	Enhancers	NHEK	skin
36	chr1:85808200-85809200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:85808200-85810400	Enhancers	Hela-S3	cervix
38	chr1:85808200-85810600	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr1:85808200-85811200	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr1:85808200-85815800	Weak transcription	Aorta	Aorta
41	chr1:85808400-85809200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:85808400-85809200	Enhancers	Psoas Muscle	Psoas
43	chr1:85808400-85810200	Enhancers	Colon Smooth Muscle	Colon
44	chr1:85808400-85810600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:85808400-85810600	Enhancers	Adipose Nuclei	Adipose
46	chr1:85808400-85811200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:85808400-85816000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:85808600-85809200	Enhancers	HSMM	muscle
49	chr1:85808600-85809400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:85808600-85809400	Flanking Active TSS	HUVEC	blood vessel

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