Variant report

Variant	rs10489509
Chromosome Location	chr1:85782270-85782271
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: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10489512	1.00[AMR][1000 genomes]
rs10873699	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11161596	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11799987	1.00[AMR][1000 genomes]
rs11802126	1.00[AMR][1000 genomes]
rs11805144	1.00[AMR][1000 genomes]
rs11805470	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11806483	1.00[AMR][1000 genomes]
rs11809053	1.00[AMR][1000 genomes]
rs11811186	1.00[AMR][1000 genomes]
rs12059670	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12071648	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082194	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17126044	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17126791	1.00[AMR][1000 genomes]
rs182845	1.00[AMR][1000 genomes]
rs20862	1.00[AMR][1000 genomes]
rs233063	1.00[AMR][1000 genomes]
rs233064	1.00[AMR][1000 genomes]
rs233122	1.00[AMR][1000 genomes]
rs233126	1.00[AMR][1000 genomes]
rs233129	1.00[AMR][1000 genomes]
rs2474121	1.00[AMR][1000 genomes]
rs41438644	1.00[AMR][1000 genomes]
rs4399206	1.00[AMR][1000 genomes]
rs57053091	1.00[AMR][1000 genomes]
rs57527592	1.00[AMR][1000 genomes]
rs57769466	1.00[AMR][1000 genomes]
rs60176254	1.00[AMR][1000 genomes]
rs60202981	1.00[AMR][1000 genomes]
rs61473029	1.00[AMR][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:69 , 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	chr1:85774800-85784000	Weak transcription	HepG2	liver
7	chr1:85774800-85790400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:85774800-85790600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:85774800-85794200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:85777400-85786400	Enhancers	NHLF	lung
11	chr1:85777600-85782400	Enhancers	HUVEC	blood vessel
12	chr1:85777600-85784000	Enhancers	NHDF-Ad	bronchial
13	chr1:85777800-85782800	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr1:85778200-85790400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:85778400-85785600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:85778600-85782600	Enhancers	HMEC	breast
17	chr1:85778800-85782400	Enhancers	NH-A	brain
18	chr1:85778800-85786000	Enhancers	NHEK	skin
19	chr1:85778800-85788800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:85778800-85789600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:85779000-85785600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:85779600-85787400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:85779800-85782800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr1:85780000-85791800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:85780000-85795800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:85780200-85790400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:85780200-85795800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:85780400-85782400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr1:85780400-85782400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:85780400-85788200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:85780400-85791600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:85780400-85793200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:85780400-85795800	Weak transcription	Gastric	stomach
34	chr1:85780800-85782400	Weak transcription	Right Atrium	heart
35	chr1:85780800-85783400	Enhancers	Fetal Brain Female	brain
36	chr1:85780800-85784000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:85780800-85786400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:85780800-85786400	Weak transcription	Right Ventricle	heart
39	chr1:85780800-85787600	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:85781000-85785600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:85781000-85785800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:85781400-85782600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:85781400-85783200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr1:85781400-85783400	Enhancers	Brain Germinal Matrix	brain
45	chr1:85781400-85783800	Weak transcription	A549	lung
46	chr1:85781400-85784200	Enhancers	Fetal Brain Male	brain
47	chr1:85781600-85782400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:85781600-85782600	Genic enhancers	Osteobl	bone
49	chr1:85781600-85782800	Genic enhancers	HSMM	muscle
50	chr1:85781600-85783200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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