Variant report

Variant	rs2002275
Chromosome Location	chr12:58283385-58283386
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58235372..58242263-chr12:58281059..58286678,18	MCF-7	breast:
2	chr12:58255415..58256919-chr12:58282201..58284913,2	MCF-7	breast:
3	chr12:58273580..58278130-chr12:58279194..58284140,7	MCF-7	breast:
4	chr12:58274036..58276456-chr12:58282278..58283846,2	MCF-7	breast:
5	chr12:58228216..58229792-chr12:58282546..58284939,2	K562	blood:
6	chr12:58281380..58284295-chr12:58284456..58286004,2	K562	blood:
7	chr12:58268216..58270366-chr12:58282645..58284163,2	MCF-7	breast:
8	chr12:58146720..58148897-chr12:58281537..58283910,2	MCF-7	breast:
9	chr12:58282101..58284820-chr8:143869710..143872581,2	MCF-7	breast:
10	chr12:58279797..58285277-chr12:58286449..58291551,8	K562	blood:
11	chr12:58281815..58283387-chr12:58288897..58291551,2	K562	blood:
12	chr12:58243942..58248184-chr12:58281468..58284195,4	MCF-7	breast:
13	chr12:58282465..58284033-chr12:58284765..58286561,2	MCF-7	breast:
14	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:
15	chr12:58281679..58287586-chr12:58288167..58292013,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000245651	Chromatin interaction
ENSG00000139266	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10444569	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10747786	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10747787	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10783850	0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs10783851	0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs10783853	1.00[ASW][hapmap]
rs10783854	0.87[AMR][1000 genomes]
rs10783855	0.80[CHD][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes]
rs10783856	0.85[AMR][1000 genomes]
rs10877024	0.82[AMR][1000 genomes]
rs10877025	0.82[AMR][1000 genomes]
rs10877026	0.81[AMR][1000 genomes]
rs10877028	0.80[CHD][hapmap];0.84[MEX][hapmap]
rs10877029	0.84[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877030	0.84[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877031	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877032	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877033	0.83[ASN][1000 genomes]
rs10877034	0.80[ASN][1000 genomes]
rs11172367	0.96[CEU][hapmap];0.90[CHD][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11172368	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172369	0.96[CEU][hapmap];0.82[CHB][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172371	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172372	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs11172375	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11172378	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs12312955	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12319233	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12426201	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1599750	0.80[CHD][hapmap];0.83[AMR][1000 genomes]
rs1599751	0.88[MEX][hapmap];0.83[AMR][1000 genomes]
rs1599931	0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1875125	0.83[AMR][1000 genomes]
rs1962047	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3751330	0.81[ASN][1000 genomes]
rs3751331	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4128707	0.81[ASN][1000 genomes]
rs4237844	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4237845	0.88[CHB][hapmap];0.93[CHD][hapmap]
rs4417327	0.80[ASN][1000 genomes]
rs4628718	0.81[ASN][1000 genomes]
rs4630335	0.94[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs4760172	0.84[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760332	0.86[ASW][hapmap];0.87[MEX][hapmap]
rs4760339	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760340	0.90[CHD][hapmap]
rs4760341	0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs5017863	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59401446	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61935769	0.81[AMR][1000 genomes]
rs6581157	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6650217	0.81[ASN][1000 genomes]
rs6650218	0.81[ASN][1000 genomes]
rs6650219	0.81[ASN][1000 genomes]
rs7134797	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7312623	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7954591	0.80[ASN][1000 genomes]
rs7954957	0.88[CHB][hapmap];0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs7969844	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7971877	0.88[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs870392	0.86[ASW][hapmap];0.87[MEX][hapmap]
rs9645819	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2002275	METTL21B	cis	Adipose Subcutaneous	GTEx
rs2002275	FAM119B	cis	cerebellum	SCAN
rs2002275	METTL21B	cis	lung	GTEx
rs2002275	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs2002275	TSFM	cis	parietal	SCAN
rs2002275	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs2002275	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs2002275	XRCC6BP1	cis	multi-tissue	Pritchard
rs2002275	XRCC6BP1	cis	Whole Blood	GTEx
rs2002275	DKFZP586D0919	cis	multi-tissue	Pritchard
rs2002275	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs2002275	CDK2	cis	parietal	SCAN
rs2002275	TSFM	cis	lymphoblastoid	seeQTL
rs2002275	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs2002275	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs2002275	FAM119B	cis	Lymphoblastoid	GTEx
rs2002275	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs2002275	XRCC6BP1	cis	Artery Tibial	GTEx
rs2002275	FAM119B	cis	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58279800-58287000	Enhancers	Fetal Stomach	stomach
2	chr12:58280200-58287400	Enhancers	Fetal Muscle Leg	muscle
3	chr12:58280400-58284400	Enhancers	Right Atrium	heart
4	chr12:58280400-58284800	Enhancers	Lung	lung
5	chr12:58280400-58288000	Enhancers	Fetal Intestine Large	intestine
6	chr12:58280600-58284800	Enhancers	Stomach Mucosa	stomach
7	chr12:58280800-58284800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:58281000-58288000	Enhancers	Fetal Muscle Trunk	muscle
9	chr12:58281400-58284400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr12:58281400-58284400	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr12:58281400-58284600	Enhancers	Fetal Heart	heart
12	chr12:58281400-58285200	Enhancers	Left Ventricle	heart
13	chr12:58281400-58287800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr12:58281400-58287800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr12:58281600-58283400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr12:58281600-58283400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:58281600-58283400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:58281600-58283400	Flanking Active TSS	NHDF-Ad	bronchial
19	chr12:58281600-58283600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:58281600-58283600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr12:58281600-58283600	Flanking Active TSS	Osteobl	bone
22	chr12:58281600-58283800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr12:58281600-58283800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:58281600-58284000	Enhancers	Fetal Thymus	thymus
25	chr12:58281600-58284000	Enhancers	Placenta Amnion	Placenta Amnion
26	chr12:58281600-58284000	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr12:58281600-58284200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:58281600-58284200	Enhancers	Adipose Nuclei	Adipose
29	chr12:58281600-58284400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:58281600-58284400	Enhancers	Right Ventricle	heart
31	chr12:58281600-58285000	Enhancers	Placenta	Placenta
32	chr12:58281600-58285000	Enhancers	Small Intestine	intestine
33	chr12:58281600-58287200	Enhancers	Fetal Intestine Small	intestine
34	chr12:58281600-58288400	Enhancers	K562	blood
35	chr12:58281800-58283400	Enhancers	H9 Cell Line	embryonic stem cell
36	chr12:58281800-58283400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:58281800-58283400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:58281800-58283400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:58281800-58283400	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr12:58281800-58283400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:58281800-58283400	Enhancers	Fetal Brain Male	brain
42	chr12:58281800-58283400	Flanking Active TSS	NHEK	skin
43	chr12:58281800-58283600	Enhancers	H1 Cell Line	embryonic stem cell
44	chr12:58281800-58283600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:58281800-58283600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:58281800-58283600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:58281800-58283600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:58281800-58283600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr12:58281800-58283800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:58281800-58283800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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