Variant report

Variant	rs62254241
Chromosome Location	chr3:69109547-69109548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:69108232..69109950-chr3:69128693..69130790,2	MCF-7	breast:
2	chr3:69099534..69103484-chr3:69106514..69109685,4	K562	blood:
3	chr3:69108014..69110452-chr3:69134129..69136532,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144746	Chromatin interaction
ENSG00000144747	Chromatin interaction
ENSG00000144744	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12632068	1.00[AFR][1000 genomes]
rs36099229	1.00[AFR][1000 genomes]
rs3772977	1.00[EUR][1000 genomes]
rs41291195	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62254187	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62255472	0.92[EUR][1000 genomes]
rs62256141	1.00[AMR][1000 genomes];0.83[EUR][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	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv520488	chr3:69104752-69114005	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69101400-69127000	Weak transcription	Small Intestine	intestine
2	chr3:69101600-69109800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:69101800-69109800	Weak transcription	Lung	lung
4	chr3:69101800-69110600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:69101800-69128400	Weak transcription	Aorta	Aorta
6	chr3:69102000-69109800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:69102000-69109800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:69102000-69109800	Weak transcription	Spleen	Spleen
9	chr3:69102000-69110400	Weak transcription	Colonic Mucosa	Colon
10	chr3:69102000-69113200	Strong transcription	HSMM	muscle
11	chr3:69102000-69128200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:69102000-69128400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:69102200-69109800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:69102200-69109800	Weak transcription	Pancreas	Pancrea
15	chr3:69102200-69109800	Weak transcription	Right Ventricle	heart
16	chr3:69102200-69110000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:69102200-69111800	Weak transcription	Stomach Mucosa	stomach
18	chr3:69102200-69113000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:69102200-69113200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:69102200-69113400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:69102200-69114000	Strong transcription	NH-A	brain
22	chr3:69102200-69127200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:69102400-69109800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:69102400-69113200	Strong transcription	Placenta	Placenta
25	chr3:69102400-69116400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:69102600-69109800	Weak transcription	Fetal Intestine Small	intestine
27	chr3:69102800-69112400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:69102800-69112600	Strong transcription	Osteobl	bone
29	chr3:69102800-69113600	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:69102800-69113800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:69102800-69116600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:69103200-69113800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:69103600-69116200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:69103800-69113400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:69103800-69113800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:69104000-69113400	Strong transcription	NHDF-Ad	bronchial
37	chr3:69104000-69113600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:69104000-69113800	Strong transcription	HUVEC	blood vessel
39	chr3:69104200-69113400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:69104400-69113400	Strong transcription	Fetal Intestine Large	intestine
41	chr3:69105200-69112400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:69105600-69112400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr3:69106200-69113400	Strong transcription	Fetal Lung	lung
44	chr3:69106800-69112600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:69107200-69112400	Strong transcription	Left Ventricle	heart
46	chr3:69107400-69110800	Strong transcription	Brain Substantia Nigra	brain
47	chr3:69107400-69112200	Strong transcription	Fetal Kidney	kidney
48	chr3:69107400-69112600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:69107400-69112600	Strong transcription	Adipose Nuclei	Adipose
50	chr3:69107400-69113600	Strong transcription	Rectal Mucosa Donor 29	rectum

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