Variant report

Variant	rs233108
Chromosome Location	chr1:85781720-85781721
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	chr1:85780416..85782774-chr1:86045761..86048333,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1001604	0.83[EUR][1000 genomes]
rs10489513	0.82[EUR][1000 genomes]
rs11161607	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161610	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11161611	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12044537	0.85[EUR][1000 genomes]
rs12047422	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12124170	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125557	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12140103	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498373	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498375	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554597	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs173026	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs18582	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1884139	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2011825	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2012683	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2177461	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2207368	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2268667	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300634	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300637	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233047	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233050	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233053	0.85[EUR][1000 genomes]
rs233054	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233055	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233057	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233058	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233059	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233060	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233061	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233062	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233066	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233067	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233068	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs233069	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233071	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233072	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs233074	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233091	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233093	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233095	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233097	0.92[EUR][1000 genomes]
rs233099	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233109	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs233112	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs233113	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233114	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233115	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233118	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233119	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233120	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233121	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233124	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233127	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233130	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233131	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233132	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233133	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2892888	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3087894	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768227	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3949301	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs423105	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949890	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949900	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6576763	0.83[EUR][1000 genomes]
rs6576764	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6576765	0.83[EUR][1000 genomes]
rs6576767	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6657817	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6671599	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66811655	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704103	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67611930	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72724606	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs761601	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs997251	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 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	chr1:85774600-85782400	Weak transcription	Fetal Intestine Small	intestine
2	chr1:85774600-85785200	Weak transcription	Liver	Liver
3	chr1:85774600-85785800	Weak transcription	Fetal Intestine Large	intestine
4	chr1:85774600-85787000	Weak transcription	Fetal Stomach	stomach
5	chr1:85774600-85794800	Weak transcription	Spleen	Spleen
6	chr1:85774800-85782200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:85774800-85782200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:85774800-85784000	Weak transcription	HepG2	liver
9	chr1:85774800-85790400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:85774800-85790600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:85774800-85794200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:85777400-85786400	Enhancers	NHLF	lung
13	chr1:85777600-85782400	Enhancers	HUVEC	blood vessel
14	chr1:85777600-85784000	Enhancers	NHDF-Ad	bronchial
15	chr1:85777800-85782800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr1:85778200-85790400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:85778400-85785600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:85778600-85782600	Enhancers	HMEC	breast
19	chr1:85778800-85781800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:85778800-85781800	Enhancers	HSMMtube	muscle
21	chr1:85778800-85782400	Enhancers	NH-A	brain
22	chr1:85778800-85786000	Enhancers	NHEK	skin
23	chr1:85778800-85788800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:85778800-85789600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:85779000-85785600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:85779400-85782000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:85779600-85787400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:85779800-85782800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:85780000-85791800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:85780000-85795800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:85780200-85782000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:85780200-85790400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:85780200-85795800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:85780400-85782200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr1:85780400-85782200	Weak transcription	Aorta	Aorta
36	chr1:85780400-85782200	Weak transcription	Left Ventricle	heart
37	chr1:85780400-85782400	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr1:85780400-85782400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:85780400-85788200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:85780400-85791600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:85780400-85793200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:85780400-85795800	Weak transcription	Gastric	stomach
43	chr1:85780800-85782200	Weak transcription	Ovary	ovary
44	chr1:85780800-85782400	Weak transcription	Right Atrium	heart
45	chr1:85780800-85783400	Enhancers	Fetal Brain Female	brain
46	chr1:85780800-85784000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:85780800-85786400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:85780800-85786400	Weak transcription	Right Ventricle	heart
49	chr1:85780800-85787600	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:85781000-85785600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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