Variant report

Variant	rs67178025
Chromosome Location	chr2:113286023-113286024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113285064..113288834-chr2:113298277..113302791,7	MCF-7	breast:
2	chr2:113284316..113286214-chr2:113288766..113291061,2	K562	blood:
3	chr2:113284781..113287040-chr2:113297336..113301005,3	K562	blood:
4	chr2:113284781..113289468-chr2:113295871..113300752,6	K562	blood:

Variant related genes	Relation type
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11679929	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987434	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12988536	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989407	1.00[ASN][1000 genomes]
rs13025468	1.00[ASN][1000 genomes]
rs1465817	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561266	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34047777	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34364366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34892661	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36086865	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3961916	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158651	1.00[ASN][1000 genomes]
rs6708841	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708927	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726169	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759275	1.00[ASN][1000 genomes]
rs71414672	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71414673	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570679	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573493	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589793	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs67178025	RGPD8	cis	Esophagus Mucosa	GTEx
rs67178025	RGPD8	cis	Thyroid	GTEx
rs67178025	RGPD8	cis	Whole Blood	GTEx
rs67178025	RGPD8	cis	lung	GTEx
rs67178025	RGPD8	cis	Nerve Tibial	GTEx
rs67178025	RGPD8	cis	Esophagus Muscularis	GTEx
rs67178025	RGPD8	cis	Muscle Skeletal	GTEx
rs67178025	RGPD8	cis	Artery Aorta	GTEx
rs67178025	RGPD8	cis	Artery Tibial	GTEx
rs67178025	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs67178025	RGPD8	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113241200-113286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:113241600-113292400	Weak transcription	Small Intestine	intestine
3	chr2:113241800-113286200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr2:113260800-113286200	Weak transcription	Fetal Brain Male	brain
5	chr2:113260800-113298800	Weak transcription	Fetal Heart	heart
6	chr2:113267400-113290000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:113268000-113286400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:113270600-113298800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:113271000-113286200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:113272600-113287400	Weak transcription	Fetal Kidney	kidney
11	chr2:113277600-113287400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:113277800-113290000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:113278200-113286200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:113279000-113299200	Weak transcription	Psoas Muscle	Psoas
15	chr2:113279600-113286200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:113280000-113286200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:113280000-113286400	Weak transcription	GM12878-XiMat	blood
18	chr2:113280200-113286200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:113280200-113286200	Weak transcription	HSMMtube	muscle
20	chr2:113280200-113286400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:113280200-113288800	Weak transcription	K562	blood
22	chr2:113280400-113286200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:113280600-113286200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:113280600-113286200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:113280600-113286200	Weak transcription	Pancreas	Pancrea
26	chr2:113280800-113286200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:113280800-113286200	Weak transcription	Brain Substantia Nigra	brain
28	chr2:113280800-113286200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:113280800-113286200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:113280800-113286200	Weak transcription	Right Ventricle	heart
31	chr2:113280800-113286200	Weak transcription	Spleen	Spleen
32	chr2:113280800-113286400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:113280800-113286400	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:113281000-113286200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:113281000-113286200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:113281000-113286200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:113281000-113286200	Weak transcription	Adipose Nuclei	Adipose
38	chr2:113281000-113286200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:113281000-113286200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:113281000-113286200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:113281000-113286400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:113281000-113286400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:113281200-113286200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:113281200-113286200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:113281200-113286200	Weak transcription	Primary B cells from cord blood	blood
46	chr2:113281200-113286200	Weak transcription	Primary T cells from cord blood	blood
47	chr2:113281200-113286200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:113281200-113286200	Weak transcription	Aorta	Aorta
49	chr2:113281200-113286200	Weak transcription	Liver	Liver
50	chr2:113281200-113286200	Weak transcription	Brain Angular Gyrus	brain

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