Variant report

Variant	rs2888288
Chromosome Location	chr12:58329935-58329936
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:418)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:418 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU2F2	chr12:58329788-58330161	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:58329558-58330228	PANC-1	pancreas:	n/a	n/a
3	USF1	chr12:58329794-58330238	ECC-1	luminal epithelium:	n/a	chr12:58330020-58330031
4	TBP	chr12:58329145-58330234	K562	blood:	n/a	chr12:58329626-58329637
5	GABPA	chr12:58329581-58330332	A549	lung:	n/a	n/a
6	POLR2A	chr12:58329821-58330237	HepG2	liver:	n/a	n/a
7	JUND	chr12:58329690-58330168	A549	lung:	n/a	chr12:58329697-58329707 chr12:58329697-58329707 chr12:58329697-58329707
8	CHD2	chr12:58329735-58330170	Hela-S3	cervix:	n/a	n/a
9	ELF1	chr12:58329578-58330368	HCT-116	colon:	n/a	chr12:58329973-58329984 chr12:58329974-58329983 chr12:58329973-58329984
10	MAX	chr12:58329879-58330179	HepG2	liver:	n/a	n/a
11	TAF1	chr12:58329559-58330209	K562	blood:	n/a	n/a
12	GABPA	chr12:58329822-58330144	HepG2	liver:	n/a	n/a
13	GATA1	chr12:58329695-58330099	K562	blood:	n/a	chr12:58329696-58329705
14	GABPA	chr12:58329649-58330186	K562	blood:	n/a	n/a
15	POLR2A	chr12:58329155-58330889	MCF10A-Er-Src	breast:	n/a	n/a
16	YY1	chr12:58329897-58330116	HCT-116	colon:	n/a	n/a
17	CHD1	chr12:58329623-58330265	GM12878	blood:	n/a	n/a
18	ETS1	chr12:58329680-58330240	A549	lung:	n/a	chr12:58330001-58330010 chr12:58330001-58330010 chr12:58329971-58329981 chr12:58329973-58329982 chr12:58330001-58330010 chr12:58329994-58330010 chr12:58329970-58329986 chr12:58329973-58329982
19	FOXP2	chr12:58329853-58330117	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr12:58329580-58330728	MCF10A-Er-Src	breast:	n/a	n/a
21	TAF1	chr12:58329703-58330324	A549	lung:	n/a	n/a
22	ZNF143	chr12:58329368-58330192	K562	blood:	n/a	n/a
23	MYC	chr12:58329849-58330128	MCF-7	breast:	n/a	n/a
24	MAZ	chr12:58329682-58330219	GM12878	blood:	n/a	n/a
25	GATA1	chr12:58329261-58330758	PBDE	blood:	n/a	chr12:58329696-58329705
26	ELF1	chr12:58329609-58330212	K562	blood:	n/a	chr12:58329973-58329984 chr12:58329974-58329983 chr12:58329973-58329984
27	BCLAF1	chr12:58329603-58330222	GM12878	blood:	n/a	chr12:58329973-58329982 chr12:58329748-58329761
28	HDAC2	chr12:58329620-58330206	MCF-7	breast:	n/a	n/a
29	TAF1	chr12:58329851-58330139	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr12:58328665-58330602	K562	blood:	n/a	n/a
31	POLR2A	chr12:58329599-58330244	GM19193	blood:	n/a	n/a
32	POLR2A	chr12:58329595-58330421	PFSK-1	brain:	n/a	n/a
33	POLR2A	chr12:58329606-58330210	GM12891	blood:	n/a	n/a
34	GABPA	chr12:58329664-58330253	MCF-7	breast:	n/a	n/a
35	POLR2A	chr12:58329704-58330194	HCT-116	colon:	n/a	n/a
36	CEBPB	chr12:58329764-58330133	K562	blood:	n/a	n/a
37	RCOR1	chr12:58329694-58330182	K562	blood:	n/a	n/a
38	SMC3	chr12:58329710-58330115	HepG2	liver:	n/a	n/a
39	E2F4	chr12:58329782-58329965	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr12:58329727-58330238	MCF-7	breast:	n/a	n/a
41	SPI1	chr12:58329717-58330259	HL-60	blood:	n/a	n/a
42	TAF1	chr12:58329686-58330214	Hela-S3	cervix:	n/a	n/a
43	PBX3	chr12:58329750-58330215	A549	lung:	n/a	chr12:58330016-58330025
44	YY1	chr12:58329819-58330236	SK-N-SH_RA	brain:	n/a	n/a
45	CREB1	chr12:58329831-58330123	A549	lung:	n/a	n/a
46	HNF4G	chr12:58329792-58330144	HepG2	liver:	n/a	n/a
47	GATA3	chr12:58329538-58330075	SH-SY5Y	brain:	n/a	chr12:58329696-58329705
48	TCF12	chr12:58329765-58330132	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr12:58329698-58330245	A549	lung:	n/a	n/a
50	EP300	chr12:58329786-58330147	HepG2	liver:	n/a	chr12:58329978-58329994 chr12:58330002-58330009 chr12:58329974-58329981

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:58329896-58329946	HRCEpiC	kidney:	n/a
2	chr12:58329896-58329946	ECC-1	luminal epithelium:	n/a
3	chr12:58329896-58329946	HCF	heart:	n/a
4	chr12:58329896-58329946	ovcar-3	ovarian:	n/a
5	chr12:58329896-58329946	SK-N-SH	brain:	n/a
6	chr12:58329896-58329946	GM19239	blood:	n/a
7	chr12:58329896-58329946	PANC-1	pancreas:	n/a
8	chr12:58329896-58329946	SKMC	muscle:	n/a
9	chr12:58329896-58329946	RPTEC	kidney:	n/a
10	chr12:58329896-58329946	ProgFib	skin:	n/a
11	chr12:58329896-58329946	MCF-7	breast:	n/a
12	chr12:58329896-58329946	GM06990	blood:	n/a
13	chr12:58329896-58329946	HMEC	breast:	n/a
14	chr12:58329896-58329946	HCT-116	colon:	n/a
15	chr12:58329896-58329946	HCPEpiC	choroid plexus:	n/a
16	chr12:58329896-58329946	H1-hESC	embryonic stem cell:	embryo
17	chr12:58329896-58329946	PFSK-1	brain:	n/a
18	chr12:58329896-58329946	HCM	heart:	n/a
19	chr12:58329896-58329946	U87	brain:	n/a
20	chr12:58329896-58329946	HepG2	liver:	n/a
21	chr12:58329896-58329946	HIPEpiC	eye:	n/a
22	chr12:58329896-58329946	SK-N-SH_RA	brain:	n/a
23	chr12:58329896-58329946	A549	lung:	n/a
24	chr12:58329896-58329946	CMK	blood:	n/a
25	chr12:58329896-58329946	AG09319	gingival:	n/a
26	chr12:58329896-58329946	Caco-2	colon:	n/a
27	chr12:58329896-58329946	HEEpiC	esophagus:	n/a
28	chr12:58329896-58329946	HRPEpiC	eye:	n/a
29	chr12:58329896-58329946	AG04450	lung:	fetal
30	chr12:58329896-58329946	SAEC	small airway:	n/a
31	chr12:58329896-58329946	NH-A	brain:	n/a
32	chr12:58329896-58329946	PrEC	prostate:	n/a
33	chr12:58329896-58329946	AG10803	skin:	n/a
34	chr12:58329896-58329946	HNPCEpiC	eye:	n/a
35	chr12:58329896-58329946	LNCaP	prostate:	n/a
36	chr12:58329896-58329946	HUVEC	blood vessel:	n/a
37	chr12:58329896-58329946	NT2-D1	testis:	n/a
38	chr12:58329896-58329946	T-47D	breast:	n/a
39	chr12:58329896-58329946	AG04449	skin:	fetal
40	chr12:58329896-58329946	NHBE	bronchial:	n/a
41	chr12:58329896-58329946	Hepatocyte	liver:	n/a
42	chr12:58329896-58329946	NHDF-neo	bronchial:	n/a
43	chr12:58329896-58329946	SK-N-MC	brain:	n/a
44	chr12:58329896-58329946	HAEpiC	amniotic membrane:	n/a
45	chr12:58329896-58329946	NB4	blood:	n/a
46	chr12:58329896-58329946	HPAEpiC	pulmonary alveolar:	n/a
47	chr12:58329896-58329946	K562	blood:	n/a
48	chr12:58329896-58329946	Hela-S3	cervix:	n/a
49	chr12:58329896-58329946	GM12878	blood:	n/a
50	chr12:58329896-58329946	HEK293	kidney:	embryo

(count:8 , 50 per page) page: 1

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

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTDSP2-2	chr12:58329622-58330391	XLOC_010102
2	lnc-CTDSP2-2	chr12:58329622-58329950	XLOC_010102
3	lnc-CTDSP2-2	chr12:58329622-58329958	ENSG00000257698.1
4	lnc-CTDSP2-2	chr12:58329624-58330625	NONHSAT028992
5	lnc-CTDSP2-2	chr12:58329622-58329947	NONHSAT028994

No data

Variant related genes	Relation type
ENSG00000257698	TF binding region
ENSG00000257698	CpG island
ENSG00000158985	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000138190	Chromatin interaction
ENSG00000037897	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10122	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10431506	0.82[CEU][hapmap]
rs10747788	0.86[CEU][hapmap]
rs10783859	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877036	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877037	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877040	0.86[CEU][hapmap]
rs11172372	0.81[JPT][hapmap]
rs11172387	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12308413	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17120057	0.84[YRI][hapmap]
rs4272820	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4335583	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4373979	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4509811	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4534624	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4583019	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4760174	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760343	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760346	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760347	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6581159	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581162	0.82[YRI][hapmap]
rs6581163	0.82[YRI][hapmap]
rs7133278	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7136981	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7295748	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7298370	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299249	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7975227	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7978588	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9971722	0.91[AMR][1000 genomes];0.91[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2888288	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs2888288	XRCC6BP1	cis	Artery Aorta	GTEx
rs2888288	XRCC6BP1	cis	lesional skin	skin_eQTL
rs2888288	XRCC6BP1	cis	lung	GTEx
rs2888288	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs2888288	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs2888288	XRCC6BP1	cis	uninvolved skin	skin_eQTL
rs2888288	XRCC6BP1	cis	Nerve Tibial	GTEx
rs2888288	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs2888288	XRCC6BP1	cis	Thyroid	GTEx
rs2888288	XRCC6BP1	cis	Stomach	GTEx
rs2888288	XRCC6BP1	cis	normal skin	skin_eQTL
rs2888288	XRCC6BP1	cis	Whole Blood	GTEx
rs2888288	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs2888288	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs2888288	XRCC6BP1	cis	Artery Tibial	GTEx
rs2888288	XRCC6BP1	cis	Heart Left Ventricle	GTEx

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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