Variant report

Variant	rs2453997
Chromosome Location	chr8:104085444-104085445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:104079134..104080797-chr8:104084707..104086213,2	MCF-7	breast:
2	chr8:104083769..104086163-chr8:104096355..104099034,2	K562	blood:
3	chr8:104083655..104086028-chr8:104086972..104089914,2	MCF-7	breast:
4	chr8:103874579..103878477-chr8:104084832..104088303,4	MCF-7	breast:
5	chr8:103922274..103923798-chr8:104084913..104086435,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253320	Chromatin interaction
ENSG00000155096	Chromatin interaction
ENSG00000253795	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1398270	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1398271	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1398272	0.80[YRI][hapmap]
rs1473820	0.90[YRI][hapmap]
rs1512350	0.80[YRI][hapmap]
rs2132863	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2132864	0.80[YRI][hapmap]
rs2248718	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453992	0.90[YRI][hapmap]
rs2453996	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454029	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2454044	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2454048	0.90[YRI][hapmap]
rs2515201	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2515205	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7844885	0.88[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831413	chr8:104085141-104269789	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2453997	BAALC	cis	cerebellum	SCAN
rs2453997	ATP6V1C1	cis	Whole Blood	GTEx
rs2453997	ATP6V1C1	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104050400-104086000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr8:104050600-104089600	Weak transcription	Psoas Muscle	Psoas
3	chr8:104051600-104087400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr8:104053200-104085600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr8:104055200-104087000	Weak transcription	K562	blood
6	chr8:104059400-104085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr8:104066800-104091200	Weak transcription	Stomach Mucosa	stomach
8	chr8:104067800-104085800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr8:104069800-104085600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr8:104069800-104085800	Weak transcription	Esophagus	oesophagus
11	chr8:104069800-104090800	Weak transcription	Aorta	Aorta
12	chr8:104072600-104086600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr8:104073400-104087600	Weak transcription	Colonic Mucosa	Colon
14	chr8:104073800-104088000	Weak transcription	Right Atrium	heart
15	chr8:104075000-104086400	Weak transcription	NHEK	skin
16	chr8:104077200-104085600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr8:104078000-104085800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr8:104079400-104087800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:104080000-104085600	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr8:104080400-104091200	Weak transcription	Small Intestine	intestine
21	chr8:104081200-104086400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr8:104081200-104088400	Weak transcription	Colon Smooth Muscle	Colon
23	chr8:104081200-104089800	Weak transcription	Left Ventricle	heart
24	chr8:104081200-104091000	Weak transcription	Ovary	ovary
25	chr8:104081600-104086000	Weak transcription	Brain Substantia Nigra	brain
26	chr8:104081800-104086400	Weak transcription	Brain Angular Gyrus	brain
27	chr8:104081800-104087400	Weak transcription	HepG2	liver
28	chr8:104082000-104089000	Weak transcription	NHLF	lung
29	chr8:104082600-104090000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr8:104082600-104090200	Weak transcription	HMEC	breast
31	chr8:104082800-104085600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr8:104083000-104085600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr8:104083000-104085800	Weak transcription	Hela-S3	cervix
34	chr8:104083200-104085800	Weak transcription	HUVEC	blood vessel
35	chr8:104083200-104089600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr8:104083200-104090200	Weak transcription	Primary B cells from cord blood	blood
37	chr8:104083200-104090600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr8:104083400-104085800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr8:104083400-104085800	Weak transcription	Brain Anterior Caudate	brain
40	chr8:104083400-104085800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr8:104083400-104085800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr8:104083400-104085800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr8:104083400-104085800	Weak transcription	Osteobl	bone
44	chr8:104083400-104086000	Weak transcription	Fetal Kidney	kidney
45	chr8:104083400-104086000	Weak transcription	Dnd41	blood
46	chr8:104083400-104086400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr8:104083400-104086400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr8:104083400-104086600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr8:104083400-104086600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr8:104083400-104088200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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