Variant report

Variant	rs62271223
Chromosome Location	chr3:134028068-134028069
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr3:134026796-134028113	IMR90	lung:	n/a	n/a
2	SMC3	chr3:134025597-134028095	SK-N-SH	brain:	n/a	chr3:134026526-134026533 chr3:134027397-134027407 chr3:134027393-134027400 chr3:134026592-134026599 chr3:134026269-134026276 chr3:134027393-134027407
3	SMC3	chr3:134026966-134028432	Hela-S3	cervix:	n/a	chr3:134027397-134027407 chr3:134027393-134027400 chr3:134027393-134027407

No.	Distal block	Cell Line	Cell type
1	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
2	chr3:134027693..134029568-chr3:134168349..134170249,2	MCF-7	breast:
3	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:
4	chr3:134027625..134034860-chr3:134199305..134206618,11	MCF-7	breast:
5	chr3:134027857..134030162-chr3:134031543..134033569,2	K562	blood:
6	chr3:134020415..134022058-chr3:134026557..134028767,2	MCF-7	breast:
7	chr3:134026798..134028420-chr3:134164621..134166613,2	MCF-7	breast:
8	chr3:134027446..134029898-chr3:134199577..134201556,2	MCF-7	breast:
9	chr3:133929711..133931992-chr3:134027528..134029983,2	MCF-7	breast:
10	chr3:134026273..134028991-chr3:134194363..134198560,4	MCF-7	breast:
11	chr3:134027069..134028938-chr3:134191393..134194235,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240006	TF binding region
ENSG00000260633	Chromatin interaction
ENSG00000182923	Chromatin interaction
ENSG00000214289	Chromatin interaction
ENSG00000114019	Chromatin interaction
ENSG00000240006	Chromatin interaction
ENSG00000129055	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10935111	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4499567	0.84[ASN][1000 genomes]
rs9854720	0.94[ASN][1000 genomes]
rs9881414	0.94[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

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134023800-134032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:134025200-134031600	Weak transcription	Ovary	ovary
3	chr3:134025600-134030800	Weak transcription	Spleen	Spleen
4	chr3:134026000-134028600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:134026000-134029200	Enhancers	HMEC	breast
6	chr3:134026200-134028400	Enhancers	NHEK	skin
7	chr3:134026400-134028800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:134026400-134029400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:134026400-134031800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:134026800-134029400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr3:134026800-134030400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:134026800-134031800	Enhancers	HSMM	muscle
13	chr3:134026800-134032400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:134026800-134034800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:134027000-134028800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:134027000-134030800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:134027000-134031000	Enhancers	Liver	Liver
18	chr3:134027000-134031400	Enhancers	Duodenum Mucosa	Duodenum
19	chr3:134027000-134031600	Enhancers	Colonic Mucosa	Colon
20	chr3:134027000-134031600	Enhancers	Placenta	Placenta
21	chr3:134027000-134032200	Enhancers	Fetal Muscle Leg	muscle
22	chr3:134027000-134032400	Enhancers	HSMMtube	muscle
23	chr3:134027000-134032400	Enhancers	NH-A	brain
24	chr3:134027200-134029400	Enhancers	Stomach Mucosa	stomach
25	chr3:134027200-134030000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:134027400-134028200	Enhancers	Fetal Kidney	kidney
27	chr3:134027400-134028400	Enhancers	H1 Cell Line	embryonic stem cell
28	chr3:134027400-134028400	Enhancers	Fetal Muscle Trunk	muscle
29	chr3:134027400-134028400	Enhancers	Stomach Smooth Muscle	stomach
30	chr3:134027400-134028600	Enhancers	Brain Cingulate Gyrus	brain
31	chr3:134027400-134028600	Enhancers	A549	lung
32	chr3:134027400-134028800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:134027400-134028800	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr3:134027400-134029000	Enhancers	Adipose Nuclei	Adipose
35	chr3:134027400-134029000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr3:134027400-134029000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr3:134027400-134029200	Enhancers	Colon Smooth Muscle	Colon
38	chr3:134027400-134029200	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr3:134027400-134029400	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr3:134027400-134029400	Enhancers	NHLF	lung
41	chr3:134027400-134029600	Enhancers	Fetal Lung	lung
42	chr3:134027400-134030200	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr3:134027400-134031400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:134027400-134031600	Enhancers	Hela-S3	cervix
45	chr3:134027400-134031800	Enhancers	Fetal Intestine Small	intestine
46	chr3:134027400-134032000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:134027400-134032000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:134027400-134032000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:134027400-134032000	Enhancers	Fetal Intestine Large	intestine
50	chr3:134027400-134032200	Enhancers	Osteobl	bone

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