Variant report

Variant	rs2372309
Chromosome Location	chr12:58329820-58329821
allele	C/T
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:9)
LncRNA
region (count:11)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58003448..58005159-chr12:58329612..58331307,2	K562	blood:
2	chr12:58329088..58329882-chr8:27471586..27472224,2	Hela-S3	cervix:
3	chr12:58329287..58330059-chr5:130599325..130600170,2	NB4	blood:
4	chr12:58164032..58167803-chr12:58328284..58330655,5	K562	blood:
5	chr10:94607840..94608395-chr12:58329411..58330143,2	NB4	blood:
6	chr12:58238134..58241883-chr12:58327269..58331955,5	K562	blood:
7	chr12:57915577..57917168-chr12:58328157..58330221,2	K562	blood:
8	chr12:58236777..58241883-chr12:58327592..58331955,7	K562	blood:
9	chr12:58158495..58161066-chr12:58329095..58330993,2	K562	blood:

(count:11 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTDSP2-2	chr12:58329624-58329929	XLOC_010102
2	lnc-CTDSP2-2	chr12:58329622-58329847	XLOC_010102
3	lnc-CTDSP2-2	chr12:58329622-58330391	XLOC_010102
4	lnc-CTDSP2-2	chr12:58329622-58329950	XLOC_010102
5	lnc-CTDSP2-2	chr12:58329622-58329958	ENSG00000257698.1
6	lnc-CTDSP2-2	chr12:58329622-58329862	ENSG00000257698.1
7	lnc-CTDSP2-2	chr12:58329622-58329846	ENSG00000257698.1
8	lnc-CTDSP2-2	chr12:58329253-58329842	ENSG00000257698.1
9	lnc-CTDSP2-2	chr12:58329624-58330625	NONHSAT028992
10	lnc-CTDSP2-2	chr12:58329622-58329947	NONHSAT028994
11	lnc-CTDSP2-2	chr12:58329622-58329933	NONHSAT028996

No data

Variant related genes	Relation type
ENSG00000158985	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000138190	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000120885	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000123427	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10431506	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783857	0.85[AMR][1000 genomes]
rs10783858	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877039	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172387	0.81[EUR][1000 genomes]
rs11172388	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172389	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751325	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3751326	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3751327	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4373979	0.81[EUR][1000 genomes]
rs4509811	0.81[EUR][1000 genomes]
rs4534624	0.81[EUR][1000 genomes]
rs4590915	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760174	0.81[EUR][1000 genomes]
rs4760344	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760346	0.80[EUR][1000 genomes]
rs6581159	0.81[CEU][hapmap]
rs7136981	0.81[EUR][1000 genomes]
rs7298370	0.81[EUR][1000 genomes]
rs7358584	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9971803	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:28)

SNP	Gene	Cis/trans	Tissue	Source
rs2372309	XRCC6BP1	cis	Artery Tibial	GTEx
rs2372309	XRCC6BP1	trans	brain	seeQTL
rs2372309	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs2372309	XRCC6BP1	cis	Stomach	GTEx
rs2372309	XRCC6BP1	cis	Thyroid	GTEx
rs2372309	XRCC6BP1	cis	normal skin	skin_eQTL
rs2372309	XRCC6BP1	cis	parietal	SCAN
rs2372309	SMARCC2	cis	cerebellum	SCAN
rs2372309	DKFZP586D0919	cis	multi-tissue	Pritchard
rs2372309	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs2372309	XRCC6BP1	cis	lung	GTEx
rs2372309	KUB3	cis	multi-tissue	Pritchard
rs2372309	XRCC6BP1	cis	uninvolved skin	skin_eQTL
rs2372309	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs2372309	FAM119B	cis	cerebellum	SCAN
rs2372309	XRCC6BP1	cis	multi-tissue	Pritchard
rs2372309	KIAA0748	cis	cerebellum	SCAN
rs2372309	XRCC6BP1	cis	brain	seeQTL
rs2372309	XRCC6BP1	cis	lesional skin	skin_eQTL
rs2372309	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs2372309	XRCC6BP1	cis	Nerve Tibial	GTEx
rs2372309	XRCC6BP1	cis	Artery Aorta	GTEx
rs2372309	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs2372309	XRCC6BP1	cis	Liver	GTEx
rs2372309	XRCC6BP1	cis	Whole Blood	GTEx
rs2372309	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs2372309	XRCC6BP1	cis	Lymphoblastoid	GTEx
rs2372309	XRCC6BP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58327600-58330000	Active TSS	Fetal Thymus	thymus
2	chr12:58327600-58330400	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr12:58327600-58330400	Active TSS	Thymus	Thymus
4	chr12:58328800-58330400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr12:58328800-58330800	Active TSS	K562	blood
6	chr12:58329000-58330200	Active TSS	HSMM	muscle
7	chr12:58329000-58330400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:58329000-58330400	Active TSS	Fetal Brain Male	brain
9	chr12:58329000-58330400	Active TSS	A549	lung
10	chr12:58329000-58330600	Active TSS	Brain Angular Gyrus	brain
11	chr12:58329200-58330200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:58329200-58330400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:58329200-58330400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:58329200-58330400	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr12:58329200-58330400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr12:58329200-58330400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:58329200-58330400	Active TSS	Colon Smooth Muscle	Colon
18	chr12:58329200-58330400	Active TSS	NHLF	lung
19	chr12:58329200-58330600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:58329200-58330600	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr12:58329200-58330600	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr12:58329200-58330600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr12:58329200-58330600	Flanking Active TSS	Liver	Liver
24	chr12:58329200-58330600	Active TSS	Psoas Muscle	Psoas
25	chr12:58329200-58330600	Active TSS	Right Atrium	heart
26	chr12:58329200-58330600	Active TSS	Right Ventricle	heart
27	chr12:58329400-58330000	Active TSS	Primary monocytes fromperipheralblood	blood
28	chr12:58329400-58330000	Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr12:58329400-58330000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:58329400-58330000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr12:58329400-58330000	Active TSS	HMEC	breast
32	chr12:58329400-58330000	Active TSS	NHEK	skin
33	chr12:58329400-58330200	Active TSS	H1 Cell Line	embryonic stem cell
34	chr12:58329400-58330200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:58329400-58330200	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr12:58329400-58330200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:58329400-58330200	Active TSS	Aorta	Aorta
38	chr12:58329400-58330200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:58329400-58330200	Active TSS	Fetal Heart	heart
40	chr12:58329400-58330200	Active TSS	Fetal Muscle Trunk	muscle
41	chr12:58329400-58330200	Active TSS	Dnd41	blood
42	chr12:58329400-58330200	Active TSS	Hela-S3	cervix
43	chr12:58329400-58330400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:58329400-58330400	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr12:58329400-58330400	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr12:58329400-58330400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:58329400-58330400	Active TSS	Brain Anterior Caudate	brain
48	chr12:58329400-58330400	Active TSS	Brain Germinal Matrix	brain
49	chr12:58329400-58330400	Active TSS	Brain Hippocampus Middle	brain
50	chr12:58329400-58330400	Active TSS	Brain Inferior Temporal Lobe	brain

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