Variant report

Variant	rs9875739
Chromosome Location	chr3:105243389-105243390
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	chr3:105239915..105242077-chr3:105242137..105244571,2	MCF-7	breast:
2	chr3:105235908..105237655-chr3:105242173..105244710,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11559013	0.87[AFR][1000 genomes]
rs13317567	0.87[AFR][1000 genomes]
rs13323843	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772558	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73854323	0.92[AFR][1000 genomes]
rs9848760	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:105222200-105260600	Weak transcription	Fetal Kidney	kidney
3	chr3:105222800-105246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:105229600-105244600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:105229600-105260400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:105230200-105262600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:105232200-105245400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:105232200-105245400	Weak transcription	NHEK	skin
10	chr3:105232200-105245600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:105232200-105274000	Weak transcription	HSMMtube	muscle
12	chr3:105233400-105250600	Weak transcription	HSMM	muscle
13	chr3:105234200-105260400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:105234600-105244000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:105234600-105244600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:105234600-105260600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:105234600-105261000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:105234600-105274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:105236200-105251000	Weak transcription	Aorta	Aorta
20	chr3:105236400-105245200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:105236400-105251000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:105237800-105243800	Weak transcription	Osteobl	bone
23	chr3:105237800-105244400	Weak transcription	Brain Angular Gyrus	brain
24	chr3:105237800-105251000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:105237800-105259000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:105237800-105274600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:105237800-105275800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr3:105238000-105244200	Weak transcription	Brain Anterior Caudate	brain
29	chr3:105238200-105244200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:105239400-105248000	Weak transcription	HUVEC	blood vessel
31	chr3:105240000-105252400	Weak transcription	Gastric	stomach
32	chr3:105240400-105243400	Enhancers	Brain Substantia Nigra	brain
33	chr3:105241000-105260400	Weak transcription	Pancreas	Pancrea
34	chr3:105241200-105250600	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr3:105241600-105250800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:105241600-105260200	Weak transcription	HepG2	liver
37	chr3:105241800-105259000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:105242000-105259800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:105242000-105293600	Weak transcription	Lung	lung
40	chr3:105242200-105252800	Weak transcription	Fetal Intestine Large	intestine
41	chr3:105242200-105259000	Weak transcription	Ovary	ovary
42	chr3:105242400-105243400	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr3:105242400-105245200	Enhancers	Brain Hippocampus Middle	brain
44	chr3:105242400-105256400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:105242400-105280400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr3:105242600-105245400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:105242800-105244000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:105242800-105245600	Weak transcription	A549	lung
49	chr3:105242800-105245600	Weak transcription	NHDF-Ad	bronchial
50	chr3:105242800-105266800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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