Variant report

Variant	rs62197748
Chromosome Location	chr2:187480006-187480007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:187474642..187476828-chr2:187479311..187482833,3	MCF-7	breast:
2	chr2:187464821..187468240-chr2:187478873..187484131,4	K562	blood:
3	chr2:187377349..187379042-chr2:187478698..187480439,2	MCF-7	breast:
4	chr2:187476119..187481022-chr2:187481523..187485481,5	K562	blood:

Variant related genes	Relation type
ENSG00000138448	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13407063	0.83[EUR][1000 genomes]
rs16828108	0.93[ASN][1000 genomes]
rs3754584	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61763608	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62197745	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS 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 target site	13 gene(s)	inside rSNPs	diseases
3	nsv875552	chr2:187393729-187505486	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2756956	chr2:187416599-187492742	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv818105	chr2:187423298-187481835	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62197748	ITGAV	cis	Muscle Skeletal	GTEx
rs62197748	AC017101.10	cis	Muscle Skeletal	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187456000-187488200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr2:187456200-187508600	Weak transcription	Esophagus	oesophagus
3	chr2:187456200-187533000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:187456400-187488200	Weak transcription	Fetal Thymus	thymus
5	chr2:187456400-187504000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:187456600-187514000	Weak transcription	Thymus	Thymus
7	chr2:187456600-187520000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:187456800-187493400	Weak transcription	Brain Germinal Matrix	brain
9	chr2:187456800-187534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:187457200-187506000	Weak transcription	Liver	Liver
11	chr2:187457200-187533800	Weak transcription	Spleen	Spleen
12	chr2:187458000-187511400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:187458000-187529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:187459400-187505600	Weak transcription	NHLF	lung
15	chr2:187460200-187506200	Weak transcription	Small Intestine	intestine
16	chr2:187460800-187486800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr2:187462600-187500600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:187462800-187515400	Weak transcription	Gastric	stomach
19	chr2:187464800-187536200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:187465800-187529200	Weak transcription	Dnd41	blood
21	chr2:187466800-187533200	Weak transcription	Colonic Mucosa	Colon
22	chr2:187467200-187528600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:187467400-187515800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:187467600-187506000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:187468800-187504000	Weak transcription	NHDF-Ad	bronchial
26	chr2:187469000-187487200	Weak transcription	Fetal Muscle Leg	muscle
27	chr2:187469000-187501800	Weak transcription	Fetal Intestine Small	intestine
28	chr2:187469400-187487000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr2:187469600-187488000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:187469600-187488200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:187470000-187487200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:187470000-187488000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:187470000-187488600	Weak transcription	Fetal Stomach	stomach
34	chr2:187470200-187482000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:187470200-187482000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:187470200-187487600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:187470200-187488600	Weak transcription	Primary T cells from cord blood	blood
38	chr2:187470400-187487200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:187470400-187487400	Weak transcription	HSMMtube	muscle
40	chr2:187471200-187487200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr2:187471400-187487200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:187471400-187487200	Weak transcription	Fetal Intestine Large	intestine
43	chr2:187471400-187487800	Weak transcription	Fetal Lung	lung
44	chr2:187471400-187488600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:187471400-187488600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:187471400-187502200	Weak transcription	NHEK	skin
47	chr2:187471600-187521000	Weak transcription	Aorta	Aorta
48	chr2:187471800-187481800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:187471800-187482000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:187471800-187487000	Weak transcription	Rectal Mucosa Donor 31	rectum

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