Variant report

Variant	rs12124170
Chromosome Location	chr1:85811182-85811183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85809927..85811661-chr1:85958885..85960854,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1001604	0.84[EUR][1000 genomes]
rs10489513	0.83[EUR][1000 genomes]
rs11161607	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161610	0.81[EUR][1000 genomes]
rs11161611	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12044537	0.86[EUR][1000 genomes]
rs12047422	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12125557	0.87[EUR][1000 genomes]
rs12140103	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1498373	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498375	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1554597	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs173026	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs18582	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1884139	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2011825	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2012683	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2177461	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2207368	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2268667	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2300634	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2300637	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233047	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233050	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs233053	0.86[EUR][1000 genomes]
rs233054	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233055	0.87[EUR][1000 genomes]
rs233057	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233058	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233059	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233060	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233061	0.91[EUR][1000 genomes]
rs233062	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs233066	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233067	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233068	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233069	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233071	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs233072	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233074	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233091	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233093	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233095	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233097	0.93[EUR][1000 genomes]
rs233099	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233108	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233109	0.92[EUR][1000 genomes]
rs233112	0.90[EUR][1000 genomes]
rs233113	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233114	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233115	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233118	0.91[EUR][1000 genomes]
rs233119	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233120	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233121	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233124	0.91[EUR][1000 genomes]
rs233127	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233130	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233131	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233132	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233133	0.91[EUR][1000 genomes]
rs2892888	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3087894	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3768227	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3949301	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs423105	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4949890	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4949900	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs506082	0.80[EUR][1000 genomes]
rs6576763	0.84[EUR][1000 genomes]
rs6576764	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6576765	0.84[EUR][1000 genomes]
rs6576766	0.81[EUR][1000 genomes]
rs6576767	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6657817	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6671599	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66811655	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704103	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67611930	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72724606	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs761601	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs997251	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85798800-85824800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:85798800-85824800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:85799000-85813600	Weak transcription	Fetal Intestine Large	intestine
4	chr1:85800400-85815000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:85805800-85811400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:85806400-85815800	Weak transcription	Pancreas	Pancrea
7	chr1:85806600-85813600	Weak transcription	Left Ventricle	heart
8	chr1:85806600-85814200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:85807600-85811200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr1:85807600-85812200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:85807600-85813400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:85807800-85811600	Enhancers	Osteobl	bone
13	chr1:85808200-85811200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:85808200-85815800	Weak transcription	Aorta	Aorta
15	chr1:85808400-85811200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:85808400-85816000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:85808600-85813600	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:85809000-85815800	Weak transcription	Ovary	ovary
19	chr1:85809200-85813600	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:85809200-85813600	Weak transcription	Psoas Muscle	Psoas
21	chr1:85809200-85814800	Weak transcription	Fetal Stomach	stomach
22	chr1:85809200-85826000	Weak transcription	Fetal Brain Female	brain
23	chr1:85809200-85838400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:85809400-85826800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:85809400-85826800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:85809600-85811200	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr1:85809600-85828800	Weak transcription	Brain Anterior Caudate	brain
28	chr1:85809800-85814800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:85809800-85815200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:85809800-85819000	Weak transcription	Brain Angular Gyrus	brain
31	chr1:85809800-85825400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:85809800-85826000	Weak transcription	Stomach Mucosa	stomach
33	chr1:85810200-85811200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:85810200-85813200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:85810200-85813600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:85810200-85813600	Weak transcription	NHLF	lung
37	chr1:85810200-85814600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:85810200-85816800	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:85810200-85823600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:85810400-85811200	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr1:85810400-85811200	Genic enhancers	HSMM	muscle
42	chr1:85810400-85811800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:85810400-85812400	Genic enhancers	NHDF-Ad	bronchial
44	chr1:85810400-85813600	Weak transcription	Liver	Liver
45	chr1:85810400-85813600	Weak transcription	Fetal Brain Male	brain
46	chr1:85810400-85813600	Weak transcription	Fetal Heart	heart
47	chr1:85810400-85813600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:85810400-85813600	Weak transcription	HepG2	liver
49	chr1:85810400-85814600	Weak transcription	Hela-S3	cervix
50	chr1:85810400-85815000	Weak transcription	Esophagus	oesophagus

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