Variant report

Variant	rs1599931
Chromosome Location	chr12:58258850-58258851
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58257328..58259688-chr12:58290813..58293614,3	MCF-7	breast:
2	chr12:58257823..58260451-chr12:58297439..58299655,2	MCF-7	breast:
3	chr12:58256926..58259595-chr12:58266193..58268490,2	K562	blood:
4	chr12:58258786..58263861-chr12:58273729..58277386,6	MCF-7	breast:
5	chr12:58254019..58259551-chr12:58280629..58287945,9	MCF-7	breast:
6	chr12:58257612..58259236-chr12:58293224..58296608,3	MCF-7	breast:
7	chr12:58255940..58258991-chr12:58263646..58265441,3	K562	blood:
8	chr12:58237213..58243657-chr12:58255578..58259317,18	MCF-7	breast:
9	chr12:58257274..58258886-chr12:58300029..58301965,2	MCF-7	breast:
10	chr12:58258378..58259324-chr2:88315828..88316518,2	Hela-S3	cervix:
11	chr12:58251247..58254157-chr12:58257386..58260333,2	K562	blood:
12	chr12:58206839..58209461-chr12:58258258..58260361,2	MCF-7	breast:
13	chr12:58258685..58259470-chr21:44299164..44299803,2	Hela-S3	cervix:
14	chr12:58257740..58261779-chr12:58273700..58278459,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135407	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000245651	Chromatin interaction
ENSG00000160193	Chromatin interaction
ENSG00000222724	Chromatin interaction
ENSG00000160194	Chromatin interaction
ENSG00000269903	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1021469	0.82[JPT][hapmap]
rs10431552	0.88[JPT][hapmap]
rs10444569	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747783	0.88[JPT][hapmap]
rs10747784	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10747786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10747787	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783847	0.88[JPT][hapmap]
rs10783848	0.86[JPT][hapmap]
rs10783850	0.93[JPT][hapmap];0.86[AMR][1000 genomes]
rs10783851	0.93[JPT][hapmap];0.86[AMR][1000 genomes]
rs10783853	1.00[YRI][hapmap]
rs10783854	0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10783855	0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10783856	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10877011	1.00[YRI][hapmap]
rs10877012	0.88[JPT][hapmap]
rs10877014	0.88[JPT][hapmap]
rs10877015	0.88[JPT][hapmap]
rs10877016	0.88[JPT][hapmap]
rs10877019	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs10877024	0.86[AMR][1000 genomes]
rs10877025	0.86[AMR][1000 genomes]
rs10877026	0.85[AMR][1000 genomes]
rs10877028	0.93[JPT][hapmap]
rs10877029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877031	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877032	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172333	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs11172335	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs11172343	0.88[JPT][hapmap]
rs11172344	0.88[JPT][hapmap]
rs11172349	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs11172351	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs11172362	0.84[AMR][1000 genomes]
rs11172367	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172368	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172369	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172371	0.82[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172375	0.81[ASN][1000 genomes]
rs11172378	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs12312955	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12319233	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12426201	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599750	0.88[JPT][hapmap];0.87[AMR][1000 genomes]
rs1599751	0.93[JPT][hapmap];0.87[AMR][1000 genomes]
rs1875124	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs1875125	0.94[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes]
rs1962047	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs2002275	0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2069502	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs2072052	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs3751331	0.83[ASN][1000 genomes]
rs3825079	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs4237844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646536	0.88[JPT][hapmap]
rs4760171	0.86[JPT][hapmap]
rs4760172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760332	0.93[JPT][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs4760335	0.80[AMR][1000 genomes]
rs4760339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760340	0.86[CHB][hapmap]
rs4760341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5017863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59401446	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581155	0.88[JPT][hapmap]
rs6581157	0.83[ASN][1000 genomes]
rs703842	0.88[JPT][hapmap]
rs7134797	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724834	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs7312623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7489290	0.92[JPT][hapmap]
rs7969844	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8181644	0.88[JPT][hapmap]
rs870392	0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs871871	0.93[JPT][hapmap]
rs923829	0.88[JPT][hapmap]
rs9645819	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1599931	XRCC6BP1	cis	Whole Blood	GTEx
rs1599931	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs1599931	METTL21B	cis	lung	GTEx
rs1599931	XRCC6BP1	cis	Artery Tibial	GTEx
rs1599931	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs1599931	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs1599931	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs1599931	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs1599931	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58256000-58259000	Weak transcription	Gastric	stomach
2	chr12:58256400-58264600	Weak transcription	Spleen	Spleen
3	chr12:58257000-58260000	Enhancers	Fetal Brain Male	brain
4	chr12:58257600-58259600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:58258000-58259000	Flanking Active TSS	HSMMtube	muscle
6	chr12:58258200-58259000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr12:58258200-58259000	Flanking Active TSS	Osteobl	bone
8	chr12:58258200-58259400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:58258400-58259000	Flanking Active TSS	Fetal Lung	lung
10	chr12:58258400-58259400	Active TSS	Aorta	Aorta
11	chr12:58258400-58259600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
12	chr12:58258400-58259600	Active TSS	Fetal Brain Female	brain
13	chr12:58258400-58259800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr12:58258600-58259000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr12:58258600-58259000	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr12:58258600-58259000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:58258600-58259000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr12:58258600-58259000	Flanking Active TSS	Fetal Heart	heart
19	chr12:58258600-58259000	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr12:58258600-58259000	Flanking Active TSS	Thymus	Thymus
21	chr12:58258600-58259000	Flanking Bivalent TSS/Enh	HepG2	liver
22	chr12:58258600-58259000	Flanking Active TSS	HUVEC	blood vessel
23	chr12:58258600-58259000	Flanking Active TSS	NHEK	skin
24	chr12:58258600-58259200	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr12:58258600-58259200	Flanking Active TSS	Fetal Muscle Trunk	muscle
26	chr12:58258600-58259400	Active TSS	Brain Anterior Caudate	brain
27	chr12:58258600-58259400	Active TSS	Brain Cingulate Gyrus	brain
28	chr12:58258600-58259400	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr12:58258600-58259600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
30	chr12:58258600-58259600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:58258600-58259600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:58258600-58259600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:58258600-58259600	Active TSS	Fetal Kidney	kidney
34	chr12:58258600-58259600	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr12:58258600-58259600	Active TSS	Ovary	ovary
36	chr12:58258600-58259600	Active TSS	Right Atrium	heart
37	chr12:58258600-58259600	Active TSS	Right Ventricle	heart
38	chr12:58258600-58259800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:58258600-58259800	Active TSS	Brain Hippocampus Middle	brain
40	chr12:58258600-58259800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:58258600-58261800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:58258600-58262000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:58258600-58262200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:58258800-58259000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
45	chr12:58258800-58259000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
46	chr12:58258800-58259000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
47	chr12:58258800-58259000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
48	chr12:58258800-58259000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr12:58258800-58259000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:58258800-58259000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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