Variant report

Variant	rs10489510
Chromosome Location	chr1:85782571-85782572
allele	C/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: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1006989	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs10747318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10782549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10873701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10873702	0.88[CEU][hapmap]
rs1146383	0.87[JPT][hapmap]
rs12022248	0.93[ASN][1000 genomes]
rs12029221	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12033483	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12034249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12035116	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12038426	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12047189	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1261681	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1342323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1357635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1357636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1391556	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1523994	0.89[CEU][hapmap]
rs1523995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1608537	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17384213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17388696	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1965876	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1975755	0.89[CEU][hapmap]
rs2016104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2037594	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2064510	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2124139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389948	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851268	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4428939	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4512701	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4631749	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949889	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4949897	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949898	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949899	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs499869	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs539714	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs600098	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs604974	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs631817	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6420965	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs659070	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6672870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72722663	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72722671	1.00[ASN][1000 genomes]
rs72722691	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72722692	0.85[AMR][1000 genomes]
rs72724608	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs731194	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7515261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7539738	0.81[EUR][1000 genomes]
rs7555670	0.84[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs990916	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85774600-85785200	Weak transcription	Liver	Liver
2	chr1:85774600-85785800	Weak transcription	Fetal Intestine Large	intestine
3	chr1:85774600-85787000	Weak transcription	Fetal Stomach	stomach
4	chr1:85774600-85794800	Weak transcription	Spleen	Spleen
5	chr1:85774800-85784000	Weak transcription	HepG2	liver
6	chr1:85774800-85790400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:85774800-85790600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:85774800-85794200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:85777400-85786400	Enhancers	NHLF	lung
10	chr1:85777600-85784000	Enhancers	NHDF-Ad	bronchial
11	chr1:85777800-85782800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr1:85778200-85790400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:85778400-85785600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:85778600-85782600	Enhancers	HMEC	breast
15	chr1:85778800-85786000	Enhancers	NHEK	skin
16	chr1:85778800-85788800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:85778800-85789600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:85779000-85785600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:85779600-85787400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:85779800-85782800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:85780000-85791800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:85780000-85795800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:85780200-85790400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:85780200-85795800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:85780400-85788200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:85780400-85791600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:85780400-85793200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:85780400-85795800	Weak transcription	Gastric	stomach
29	chr1:85780800-85783400	Enhancers	Fetal Brain Female	brain
30	chr1:85780800-85784000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:85780800-85786400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:85780800-85786400	Weak transcription	Right Ventricle	heart
33	chr1:85780800-85787600	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:85781000-85785600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:85781000-85785800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:85781400-85782600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:85781400-85783200	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr1:85781400-85783400	Enhancers	Brain Germinal Matrix	brain
39	chr1:85781400-85783800	Weak transcription	A549	lung
40	chr1:85781400-85784200	Enhancers	Fetal Brain Male	brain
41	chr1:85781600-85782600	Genic enhancers	Osteobl	bone
42	chr1:85781600-85782800	Genic enhancers	HSMM	muscle
43	chr1:85781600-85783200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:85781800-85783600	Weak transcription	Hela-S3	cervix
45	chr1:85781800-85783800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:85781800-85786000	Weak transcription	Placenta	Placenta
47	chr1:85781800-85786400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:85781800-85792800	Weak transcription	Pancreas	Pancrea
49	chr1:85782000-85782600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:85782000-85783400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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