Variant report

Variant	rs6741839
Chromosome Location	chr2:39749311-39749312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39744597..39747139-chr2:39748904..39750749,2	MCF-7	breast:
2	chr2:39742944..39745586-chr2:39749243..39752053,2	K562	blood:
3	chr2:39749162..39751923-chr2:39751985..39754949,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11124685	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11124686	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1526024	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56337010	0.89[EUR][1000 genomes]
rs6753798	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs714855	0.83[ASN][1000 genomes]
rs72803115	0.89[EUR][1000 genomes]
rs734663	0.88[EUR][1000 genomes]
rs7565507	0.81[ASN][1000 genomes]
rs7591326	0.81[AMR][1000 genomes];0.88[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	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39724800-39750600	Weak transcription	Gastric	stomach
2	chr2:39743000-39750200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:39744200-39753200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:39744800-39749800	Weak transcription	Osteobl	bone
5	chr2:39744800-39751200	Weak transcription	Right Ventricle	heart
6	chr2:39745000-39749600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:39745000-39749800	Weak transcription	Right Atrium	heart
8	chr2:39745000-39749800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:39745000-39751000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:39745000-39752000	Weak transcription	Brain Angular Gyrus	brain
11	chr2:39745200-39750200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:39746000-39750200	Weak transcription	Fetal Heart	heart
13	chr2:39747400-39749800	ZNF genes & repeats	HepG2	liver
14	chr2:39747800-39749400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
15	chr2:39747800-39751200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
16	chr2:39748000-39749400	ZNF genes & repeats	Fetal Intestine Small	intestine
17	chr2:39748000-39750600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
18	chr2:39748200-39749400	ZNF genes & repeats	Placenta	Placenta
19	chr2:39748400-39749400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:39748400-39749400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:39748400-39749800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:39748400-39753600	Enhancers	Psoas Muscle	Psoas
23	chr2:39748600-39749400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:39748600-39749400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:39748600-39749400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
26	chr2:39748600-39749400	ZNF genes & repeats	Fetal Muscle Leg	muscle
27	chr2:39748600-39750000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
28	chr2:39748600-39753400	Enhancers	Left Ventricle	heart
29	chr2:39748800-39749400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr2:39748800-39749400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
31	chr2:39748800-39753000	Enhancers	Stomach Smooth Muscle	stomach
32	chr2:39749000-39749400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:39749000-39750400	Weak transcription	Aorta	Aorta
34	chr2:39749000-39752200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:39749200-39749800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:39749200-39749800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:39749200-39749800	Weak transcription	Fetal Stomach	stomach
38	chr2:39749200-39749800	Weak transcription	HSMMtube	muscle
39	chr2:39749200-39750000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:39749200-39750000	Weak transcription	NHLF	lung
41	chr2:39749200-39750200	Weak transcription	Adipose Nuclei	Adipose
42	chr2:39749200-39750400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:39749200-39750400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:39749200-39750800	Enhancers	Liver	Liver
45	chr2:39749200-39751200	Weak transcription	Fetal Muscle Trunk	muscle

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