Variant report

Variant	rs4974487
Chromosome Location	chr3:134051961-134051962
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	chr3:134025978..134037323-chr3:134040972..134053086,34	MCF-7	breast:
2	chr3:134048500..134051081-chr3:134051265..134053947,2	K562	blood:

Variant related genes	Relation type
ENSG00000240006	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1111516	0.84[ASN][1000 genomes]
rs11719057	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1466827	0.80[ASN][1000 genomes]
rs1498731	0.84[ASN][1000 genomes]
rs1603824	0.84[ASN][1000 genomes]
rs2133307	0.84[ASN][1000 genomes]
rs2400278	0.84[ASN][1000 genomes]
rs2400279	0.84[ASN][1000 genomes]
rs2400280	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34341902	0.84[ASN][1000 genomes]
rs35951257	0.84[ASN][1000 genomes]
rs4264700	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4974485	0.84[ASN][1000 genomes]
rs4974489	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4974491	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4974494	0.84[ASN][1000 genomes]
rs4974495	0.84[ASN][1000 genomes]
rs4974496	0.82[ASN][1000 genomes]
rs4974497	0.84[ASN][1000 genomes]
rs6439477	0.84[ASN][1000 genomes]
rs6786148	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450	0.84[ASN][1000 genomes]
rs9817900	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9853621	0.92[EUR][1000 genomes];0.89[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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4974487	RP11-375I20.6	cis	Thyroid	GTEx
rs4974487	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs4974487	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134035000-134058800	Weak transcription	Liver	Liver
2	chr3:134041200-134056600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:134042000-134060800	Enhancers	Placenta	Placenta
4	chr3:134042200-134052400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:134042600-134054000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:134042600-134054400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:134042800-134057000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:134044000-134054400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr3:134045000-134056400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:134045400-134052600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:134046000-134052400	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:134046400-134052600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:134046600-134053000	Weak transcription	Spleen	Spleen
14	chr3:134046600-134053600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:134047400-134053200	Weak transcription	Psoas Muscle	Psoas
16	chr3:134047400-134054000	Enhancers	NH-A	brain
17	chr3:134047600-134054200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:134048400-134054000	Enhancers	Aorta	Aorta
19	chr3:134048600-134053800	Weak transcription	HUVEC	blood vessel
20	chr3:134048600-134054200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:134048800-134052200	Enhancers	HepG2	liver
22	chr3:134049000-134054200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:134049000-134054200	Enhancers	Rectal Smooth Muscle	rectum
24	chr3:134049000-134054600	Enhancers	Fetal Muscle Leg	muscle
25	chr3:134049200-134060800	Enhancers	Fetal Intestine Large	intestine
26	chr3:134049400-134052800	Enhancers	Fetal Heart	heart
27	chr3:134049400-134054200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:134049600-134052800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:134049600-134054400	Enhancers	H9 Cell Line	embryonic stem cell
30	chr3:134049600-134054400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:134049600-134054600	Enhancers	Fetal Stomach	stomach
32	chr3:134049600-134054600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr3:134049600-134054800	Enhancers	Lung	lung
34	chr3:134049800-134053600	Enhancers	Fetal Muscle Trunk	muscle
35	chr3:134049800-134054200	Enhancers	Ovary	ovary
36	chr3:134049800-134054400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr3:134050200-134054400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:134050600-134053000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:134050600-134056200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:134050600-134057000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:134050600-134060400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:134050800-134054000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:134050800-134054200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr3:134050800-134054800	Enhancers	Colon Smooth Muscle	Colon
45	chr3:134050800-134061000	Weak transcription	Fetal Brain Female	brain
46	chr3:134051000-134052000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:134051000-134052000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:134051000-134052000	Weak transcription	Fetal Intestine Small	intestine
49	chr3:134051000-134052200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:134051000-134053600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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