Variant report

Variant	rs4272820
Chromosome Location	chr12:58330541-58330542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58330309-58330697	GM12892	blood:	n/a	n/a
2	POLR2A	chr12:58329155-58330889	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:58329580-58330728	MCF10A-Er-Src	breast:	n/a	n/a
4	GATA1	chr12:58329261-58330758	PBDE	blood:	n/a	chr12:58329696-58329705
5	POLR2A	chr12:58328665-58330602	K562	blood:	n/a	n/a
6	POLR2A	chr12:58329663-58330691	GM12892	blood:	n/a	n/a
7	POLR2A	chr12:58329433-58330739	K562	blood:	n/a	n/a
8	POLR2A	chr12:58328701-58331022	GM12891	blood:	n/a	n/a
9	MTA3	chr12:58329538-58330752	GM12878	blood:	n/a	n/a
10	MYC	chr12:58329633-58330569	NB4	blood:	n/a	n/a
11	POLR2A	chr12:58329727-58330629	MCF-7	breast:	n/a	n/a
12	GABPA	chr12:58329380-58330604	MCF-7	breast:	n/a	n/a
13	ZNF274	chr12:58330263-58331012	K562	blood:	n/a	n/a
14	POLR2A	chr12:58328536-58330720	K562	blood:	n/a	n/a
15	POLR2A	chr12:58328611-58330747	K562	blood:	n/a	n/a
16	POLR2A	chr12:58329454-58330640	U87	brain:	n/a	n/a
17	IRF1	chr12:58328806-58330914	K562	blood:	n/a	chr12:58330860-58330873
18	REST	chr12:58329412-58330543	H1-neurons	neurons:	n/a	chr12:58329736-58329749
19	POLR2A	chr12:58329620-58330643	GM12878	blood:	n/a	n/a
20	HCFC1	chr12:58329176-58330988	Hela-S3	cervix:	n/a	n/a
21	GABPA	chr12:58329393-58330558	A549	lung:	n/a	n/a
22	MXI1	chr12:58329025-58330799	SK-N-SH	brain:	n/a	chr12:58329896-58329911 chr12:58329898-58329913
23	POLR2A	chr12:58329448-58330687	U87	brain:	n/a	n/a
24	POLR2A	chr12:58329616-58330711	GM12878	blood:	n/a	n/a
25	POLR2A	chr12:58329582-58330704	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr12:58328011-58330782	K562	blood:	n/a	n/a
27	POLR2A	chr12:58329115-58330574	Raji	blood:	n/a	n/a
28	JUND	chr12:58329224-58330659	K562	blood:	n/a	chr12:58329697-58329707 chr12:58329697-58329707 chr12:58329697-58329707
29	POLR2A	chr12:58330339-58330847	K562	blood:	n/a	n/a
30	POLR2A	chr12:58328674-58330767	NB4	blood:	n/a	n/a
31	POLR2A	chr12:58328501-58330747	HL-60	blood:	n/a	n/a
32	POLR2A	chr12:58329530-58330631	GM19099	blood:	n/a	n/a
33	ZC3H11A	chr12:58329820-58330663	K562	blood:	n/a	n/a
34	POLR2A	chr12:58329561-58330640	GM12892	blood:	n/a	n/a
35	POLR2A	chr12:58328672-58330754	K562	blood:	n/a	n/a
36	POLR2A	chr12:58329491-58330580	K562	blood:	n/a	n/a
37	POLR2A	chr12:58329619-58330679	GM18505	blood:	n/a	n/a
38	POLR2A	chr12:58328298-58330708	PBDE	blood:	n/a	n/a
39	MAFF	chr12:58329618-58330754	K562	blood:	n/a	n/a
40	EP300	chr12:58328672-58330669	K562	blood:	n/a	chr12:58329978-58329994 chr12:58329736-58329752 chr12:58330002-58330009 chr12:58329974-58329981
41	MAFK	chr12:58329538-58330575	K562	blood:	n/a	n/a
42	RCOR1	chr12:58330502-58330632	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58003448..58005159-chr12:58329612..58331307,2	K562	blood:
2	chr12:58146721..58149123-chr12:58330314..58332676,2	K562	blood:
3	chr12:58164032..58167803-chr12:58328284..58330655,5	K562	blood:
4	chr12:58238134..58241883-chr12:58327269..58331955,5	K562	blood:
5	chr12:58236777..58241883-chr12:58327592..58331955,7	K562	blood:
6	chr12:58158495..58161066-chr12:58329095..58330993,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTDSP2-2	chr12:58329624-58330625	NONHSAT028992

Variant related genes	Relation type
ENSG00000257698	TF binding region
XRCC6BP1	TF binding region
ENSG00000240771	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000139266	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000037897	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10122	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10431506	0.85[CEU][hapmap]
rs10747788	0.82[CEU][hapmap]
rs10783859	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877036	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877037	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877040	0.82[CEU][hapmap]
rs11172372	0.81[JPT][hapmap]
rs11172387	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12308413	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2888288	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4335583	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4373979	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4509811	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4534624	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4583019	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760174	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760343	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760346	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760347	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6581159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7133278	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136981	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7295748	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7298370	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7299249	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7975227	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7978588	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9971722	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4272820	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs4272820	XRCC6BP1	cis	Thyroid	GTEx
rs4272820	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4272820	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs4272820	XRCC6BP1	cis	Artery Aorta	GTEx
rs4272820	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs4272820	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs4272820	XRCC6BP1	cis	lung	GTEx
rs4272820	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs4272820	XRCC6BP1	cis	Whole Blood	GTEx
rs4272820	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs4272820	XRCC6BP1	cis	Nerve Tibial	GTEx
rs4272820	XRCC6BP1	cis	Artery Tibial	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58328800-58330800	Active TSS	K562	blood
2	chr12:58329000-58330600	Active TSS	Brain Angular Gyrus	brain
3	chr12:58329200-58330600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:58329200-58330600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr12:58329200-58330600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr12:58329200-58330600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr12:58329200-58330600	Flanking Active TSS	Liver	Liver
8	chr12:58329200-58330600	Active TSS	Psoas Muscle	Psoas
9	chr12:58329200-58330600	Active TSS	Right Atrium	heart
10	chr12:58329200-58330600	Active TSS	Right Ventricle	heart
11	chr12:58329400-58330600	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr12:58329400-58330600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:58329400-58330600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:58329400-58330600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:58329400-58330600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:58329400-58330600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:58329400-58330600	Active TSS	Brain Cingulate Gyrus	brain
18	chr12:58329400-58330800	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr12:58329400-58330800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:58329400-58330800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:58329600-58330800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:58330000-58330600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr12:58330000-58330600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:58330000-58330600	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr12:58330000-58330600	Flanking Active TSS	HMEC	breast
26	chr12:58330200-58330600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr12:58330200-58330600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:58330200-58330600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:58330200-58330600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr12:58330200-58330600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr12:58330200-58330600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr12:58330200-58330600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr12:58330200-58330600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:58330200-58330600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:58330200-58330600	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr12:58330200-58330600	Enhancers	Fetal Heart	heart
37	chr12:58330200-58330600	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr12:58330200-58330600	Enhancers	Stomach Mucosa	stomach
39	chr12:58330200-58330600	Flanking Active TSS	HSMM	muscle
40	chr12:58330200-58330600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr12:58330200-58330800	Enhancers	Primary B cells from peripheral blood	blood
42	chr12:58330200-58330800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:58330200-58330800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:58330200-58330800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:58330200-58330800	Flanking Active TSS	Dnd41	blood
46	chr12:58330200-58330800	Flanking Active TSS	Hela-S3	cervix
47	chr12:58330200-58334400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr12:58330200-58334400	Weak transcription	Colonic Mucosa	Colon
49	chr12:58330200-58334400	Weak transcription	Small Intestine	intestine
50	chr12:58330200-58334600	Weak transcription	Esophagus	oesophagus

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