Variant report

Variant	rs10054139
Chromosome Location	chr5:60759515-60759516
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	chr5:60755091..60757067-chr5:60758123..60759831,2	K562	blood:
2	chr5:60749146..60750936-chr5:60757361..60759917,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10051279	0.83[AFR][1000 genomes]
rs10052429	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10055806	0.93[YRI][hapmap]
rs10060985	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10073626	0.83[AFR][1000 genomes]
rs10471270	0.83[AFR][1000 genomes]
rs12332333	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1867729	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28640139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55772332	0.83[AFR][1000 genomes]
rs59299298	0.83[AFR][1000 genomes]
rs6878812	0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73107461	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73107471	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73107480	0.93[AFR][1000 genomes];1.00[AMR][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	esv2753894	chr5:60731458-60777345	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
2	nsv522826	chr5:60754419-60759524	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60744400-60767800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr5:60746000-60759600	Weak transcription	Aorta	Aorta
3	chr5:60746200-60759800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:60747000-60760600	Weak transcription	NHLF	lung
5	chr5:60747000-60762800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:60747200-60760200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:60747600-60760400	Weak transcription	NH-A	brain
8	chr5:60747600-60770600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:60749000-60762200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:60750000-60760400	Weak transcription	Primary T cells from cord blood	blood
11	chr5:60751600-60760400	Weak transcription	Right Atrium	heart
12	chr5:60752600-60760200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:60753000-60760200	Weak transcription	Adipose Nuclei	Adipose
14	chr5:60753200-60760200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:60755000-60762600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:60755600-60762600	Enhancers	Brain Substantia Nigra	brain
17	chr5:60756400-60760400	Weak transcription	Brain Angular Gyrus	brain
18	chr5:60756800-60761000	Enhancers	Brain Anterior Caudate	brain
19	chr5:60757000-60761600	Enhancers	Brain Hippocampus Middle	brain
20	chr5:60757400-60759800	Weak transcription	Left Ventricle	heart
21	chr5:60757400-60760000	Enhancers	Colon Smooth Muscle	Colon
22	chr5:60757400-60760200	Weak transcription	Colonic Mucosa	Colon
23	chr5:60757400-60760200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr5:60757400-60760400	Weak transcription	Gastric	stomach
25	chr5:60757600-60759600	Weak transcription	Pancreas	Pancrea
26	chr5:60757600-60759600	Weak transcription	Psoas Muscle	Psoas
27	chr5:60757600-60759600	Weak transcription	Small Intestine	intestine
28	chr5:60757600-60759800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr5:60757600-60760200	Weak transcription	Esophagus	oesophagus
30	chr5:60757600-60771000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:60757800-60760200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:60757800-60760200	Weak transcription	HSMM	muscle
33	chr5:60757800-60760600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr5:60757800-60760800	Enhancers	HSMMtube	muscle
35	chr5:60758000-60759600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr5:60758000-60760200	Weak transcription	Liver	Liver
37	chr5:60758000-60760200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr5:60758000-60760400	Weak transcription	Fetal Kidney	kidney
39	chr5:60758000-60764000	Weak transcription	Fetal Intestine Small	intestine
40	chr5:60758000-60772800	Weak transcription	Fetal Intestine Large	intestine
41	chr5:60758200-60760400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:60758200-60761000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:60758200-60762200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr5:60758200-60762800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:60758200-60763200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:60758400-60760400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:60758600-60760400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr5:60759000-60761000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:60759200-60759800	Enhancers	Fetal Heart	heart
50	chr5:60759200-60760400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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