Variant report

Variant	rs11172378
Chromosome Location	chr12:58298161-58298162
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58228517..58230592-chr12:58298078..58299845,2	MCF-7	breast:
2	chr12:58239081..58242355-chr12:58294578..58298218,3	K562	blood:
3	chr12:58164497..58167475-chr12:58297989..58300788,2	K562	blood:
4	chr12:58238316..58242683-chr12:58295473..58302602,14	MCF-7	breast:
5	chr12:58225549..58227455-chr12:58294861..58299199,3	MCF-7	breast:
6	chr12:58297630..58299144-chr12:58332422..58334699,2	K562	blood:
7	chr12:58236196..58241196-chr12:58294118..58300852,8	MCF-7	breast:
8	chr12:58257823..58260451-chr12:58297439..58299655,2	MCF-7	breast:
9	chr12:58233992..58236447-chr12:58297834..58300424,2	K562	blood:
10	chr12:58239569..58244482-chr12:58295741..58298218,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257921	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10444569	0.82[ASN][1000 genomes]
rs10747786	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs10747787	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs10877029	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs10877030	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs10877031	0.82[ASN][1000 genomes]
rs10877032	0.82[ASN][1000 genomes]
rs10877033	0.80[ASN][1000 genomes]
rs10877034	0.80[ASN][1000 genomes]
rs11172367	0.87[CHD][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs11172368	0.81[ASN][1000 genomes]
rs11172369	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs11172371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11172372	0.88[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11172375	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12319233	0.82[ASN][1000 genomes]
rs12426201	0.81[ASN][1000 genomes]
rs1599931	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs1962047	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2002275	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs3751330	0.83[ASN][1000 genomes]
rs3751331	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4128707	0.83[ASN][1000 genomes]
rs4237844	0.82[CHB][hapmap];0.87[CHD][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs4237845	0.88[CHB][hapmap];0.97[CHD][hapmap];0.80[ASN][1000 genomes]
rs4628718	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4630335	0.92[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760172	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs4760339	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs4760340	0.87[CHD][hapmap]
rs4760341	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs61935769	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6581157	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6650217	0.83[ASN][1000 genomes]
rs6650218	0.83[ASN][1000 genomes]
rs6650219	0.83[ASN][1000 genomes]
rs7306124	0.84[EUR][1000 genomes]
rs7312623	0.82[CHB][hapmap];0.90[CHD][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs7954591	0.83[ASN][1000 genomes]
rs7954957	0.88[CHB][hapmap];0.97[CHD][hapmap];0.83[ASN][1000 genomes]
rs7963992	0.82[ASN][1000 genomes]
rs7969844	0.81[ASN][1000 genomes]
rs7971877	0.88[CHB][hapmap];0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs9645819	0.81[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs11172378	XRCC6BP1	cis	Nerve Tibial	GTEx
rs11172378	XRCC6BP1	cis	lung	GTEx
rs11172378	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs11172378	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs11172378	FAM119B	cis	lymphoblastoid	seeQTL
rs11172378	XRCC6BP1	cis	Whole Blood	GTEx
rs11172378	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs11172378	FAM119B	cis	cerebellum	SCAN
rs11172378	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs11172378	XRCC6BP1	cis	Artery Aorta	GTEx
rs11172378	XRCC6BP1	cis	Artery Tibial	GTEx
rs11172378	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs11172378	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs11172378	STAT6	cis	parietal	SCAN
rs11172378	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs11172378	XRCC6BP1	cis	Thyroid	GTEx
rs11172378	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58292800-58298800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:58292800-58299000	Weak transcription	Fetal Kidney	kidney
3	chr12:58292800-58299000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:58293200-58298800	Weak transcription	Adipose Nuclei	Adipose
5	chr12:58293200-58298800	Weak transcription	Placenta	Placenta
6	chr12:58293200-58299000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:58293200-58299000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:58293200-58299000	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:58293200-58299000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:58293200-58299000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:58293200-58299000	Weak transcription	Brain Substantia Nigra	brain
12	chr12:58293200-58299000	Weak transcription	Fetal Lung	lung
13	chr12:58293200-58299000	Weak transcription	A549	lung
14	chr12:58293200-58299000	Weak transcription	NHDF-Ad	bronchial
15	chr12:58293400-58298800	Weak transcription	Hela-S3	cervix
16	chr12:58293400-58299000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:58293400-58299000	Weak transcription	Brain Anterior Caudate	brain
18	chr12:58293400-58299000	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:58293400-58299000	Weak transcription	Fetal Stomach	stomach
20	chr12:58293400-58299000	Weak transcription	K562	blood
21	chr12:58293800-58298800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:58293800-58299000	Weak transcription	Primary T cells from cord blood	blood
23	chr12:58293800-58299000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:58293800-58299000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:58293800-58299000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:58293800-58299000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:58293800-58299000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr12:58293800-58299000	Weak transcription	HMEC	breast
29	chr12:58294000-58299000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:58294000-58299000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:58294000-58299000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:58294000-58299000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:58294000-58299000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:58294000-58299000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:58294000-58299000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:58294000-58299000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:58294200-58298200	Weak transcription	Fetal Thymus	thymus
38	chr12:58294200-58298800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr12:58294200-58298800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:58294200-58299000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:58294400-58298800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr12:58294400-58299000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:58294600-58299000	Weak transcription	GM12878-XiMat	blood
44	chr12:58296600-58298800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr12:58296800-58299000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:58296800-58299000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:58296800-58299000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:58296800-58299000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:58296800-58299000	Weak transcription	Osteobl	bone
50	chr12:58296800-58299200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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