Variant report

Variant	rs60348850
Chromosome Location	chr2:112821880-112821881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:112819853..112822054-chr2:113032254..113034904,2	K562	blood:
2	chr2:112812985..112814670-chr2:112820639..112822288,2	K562	blood:
3	chr2:112728900..112731202-chr2:112820823..112823636,2	K562	blood:
4	chr2:112820549..112822093-chr2:112840179..112842837,2	K562	blood:
5	chr2:112815166..112819031-chr2:112819758..112824247,10	K562	blood:
6	chr2:112819853..112822775-chr2:113032254..113034954,2	K562	blood:
7	chr2:112819134..112821985-chr2:112825483..112827864,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000188177	Chromatin interaction
ENSG00000153214	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs3811642	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4525701	0.83[EUR][1000 genomes]
rs55641603	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6717702	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67923925	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7567842	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60348850	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112814200-112827000	Weak transcription	Psoas Muscle	Psoas
2	chr2:112814200-112835400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:112814200-112849800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:112814200-112859800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:112814400-112831600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:112814600-112829400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:112814800-112823800	Weak transcription	Brain Substantia Nigra	brain
8	chr2:112814800-112826800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:112814800-112832200	Weak transcription	A549	lung
10	chr2:112814800-112842000	Weak transcription	Fetal Heart	heart
11	chr2:112815000-112822000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:112815000-112824000	Weak transcription	Brain Germinal Matrix	brain
13	chr2:112815200-112822200	Weak transcription	Pancreas	Pancrea
14	chr2:112815200-112823200	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:112815200-112823600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:112815200-112823600	Weak transcription	Fetal Brain Male	brain
17	chr2:112815200-112833200	Weak transcription	Hela-S3	cervix
18	chr2:112815800-112822600	Strong transcription	HSMM	muscle
19	chr2:112816000-112825000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:112816000-112833800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:112816400-112822200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:112816400-112823000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr2:112816400-112827200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr2:112816400-112829600	Strong transcription	Placenta	Placenta
25	chr2:112816600-112822200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:112816600-112825200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:112816600-112834200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr2:112816600-112866200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr2:112816800-112823200	Strong transcription	Osteobl	bone
30	chr2:112816800-112871400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr2:112817000-112827000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:112817000-112827400	Strong transcription	Fetal Stomach	stomach
33	chr2:112817000-112830200	Strong transcription	Fetal Muscle Leg	muscle
34	chr2:112817200-112822600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:112817200-112822800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:112817200-112823000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:112817200-112823000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:112817200-112823400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:112817200-112824800	Weak transcription	Stomach Mucosa	stomach
40	chr2:112817200-112825200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:112817400-112824800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:112817400-112827800	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr2:112817400-112835400	Weak transcription	Esophagus	oesophagus
44	chr2:112817400-112835400	Weak transcription	Right Ventricle	heart
45	chr2:112817600-112824000	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr2:112818000-112822600	Strong transcription	NHDF-Ad	bronchial
47	chr2:112818200-112829800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:112818400-112822400	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr2:112818400-112822400	Strong transcription	Rectal Smooth Muscle	rectum
50	chr2:112818400-112827200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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