Variant report

Variant	rs12528822
Chromosome Location	chr6:109661541-109661542
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	UBTF	chr6:109661517-109661830	K562	blood:	n/a	n/a
2	GATA1	chr6:109661041-109662010	PBDE	blood:	n/a	chr6:109661720-109661729
3	CEBPB	chr6:109661378-109661843	K562	blood:	n/a	n/a
4	EP300	chr6:109661342-109661928	K562	blood:	n/a	n/a
5	PML	chr6:109661444-109661872	K562	blood:	n/a	n/a
6	RFX5	chr6:109661499-109661695	K562	blood:	n/a	n/a
7	TAL1	chr6:109661416-109661954	K562	blood:	n/a	n/a
8	CCNT2	chr6:109661498-109661721	K562	blood:	n/a	n/a
9	GATA2	chr6:109661263-109661556	SH-SY5Y	brain:	n/a	n/a
10	RCOR1	chr6:109661470-109661849	K562	blood:	n/a	n/a
11	RCOR1	chr6:109661496-109661967	K562	blood:	n/a	n/a
12	CUX1	chr6:109661342-109661885	K562	blood:	n/a	n/a
13	TEAD4	chr6:109661430-109661960	K562	blood:	n/a	n/a
14	MYC	chr6:109661481-109661938	K562	blood:	n/a	n/a
15	MYC	chr6:109661514-109661929	K562	blood:	n/a	n/a
16	TEAD4	chr6:109661338-109662023	K562	blood:	n/a	n/a
17	NR2F2	chr6:109661518-109662108	K562	blood:	n/a	n/a
18	GATA3	chr6:109661262-109661612	T-47D	breast:	n/a	n/a
19	CBX3	chr6:109661401-109661883	K562	blood:	n/a	n/a
20	ZMIZ1	chr6:109661536-109661821	K562	blood:	n/a	n/a
21	TBL1XR1	chr6:109661443-109661865	K562	blood:	n/a	n/a
22	EP300	chr6:109661486-109661826	K562	blood:	n/a	n/a
23	GATA2	chr6:109661442-109661953	K562	blood:	n/a	chr6:109661720-109661729
24	BHLHE40	chr6:109661378-109661904	K562	blood:	n/a	n/a
25	JUND	chr6:109661364-109661896	K562	blood:	n/a	chr6:109661718-109661729
26	NR2F2	chr6:109661530-109661916	K562	blood:	n/a	n/a
27	CEBPB	chr6:109661315-109661760	K562	blood:	n/a	n/a
28	ARID3A	chr6:109661341-109662200	K562	blood:	n/a	n/a
29	MAFK	chr6:109661522-109661928	K562	blood:	n/a	chr6:109661784-109661800 chr6:109661723-109661732
30	IRF1	chr6:109661353-109661812	K562	blood:	n/a	n/a
31	ATF1	chr6:109661358-109661845	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109660514..109663248-chr6:109671174..109674117,2	K562	blood:
2	chr6:109624816..109627658-chr6:109659263..109661556,2	K562	blood:
3	chr6:109655737..109658352-chr6:109659760..109662191,3	K562	blood:
4	chr6:109659415..109661984-chr6:109702237..109705687,4	MCF-7	breast:
5	chr6:109656032..109659893-chr6:109659967..109664099,6	MCF-7	breast:
6	chr6:109635700..109637262-chr6:109660535..109662631,2	K562	blood:
7	chr6:109615706..109617299-chr6:109661071..109663820,2	MCF-7	breast:
8	chr6:109571423..109573781-chr6:109659713..109661931,2	MCF-7	breast:
9	chr6:109660483..109663037-chr6:109663413..109665260,2	K562	blood:

No data

Variant related genes	Relation type
CCDC162P	TF binding region
ENSG00000203799	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000201023	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10080429	0.89[EUR][1000 genomes]
rs1040284	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10457190	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10457194	0.82[CHB][hapmap]
rs10457195	0.82[CHB][hapmap]
rs1048203	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10782161	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10782162	0.95[CEU][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs10872032	0.93[EUR][1000 genomes]
rs10872034	0.82[EUR][1000 genomes]
rs11153171	0.86[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs11153174	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11153175	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11153176	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11153177	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11153180	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11153181	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11153183	0.82[CHB][hapmap]
rs11251	0.84[MKK][hapmap]
rs11753645	0.84[CEU][hapmap]
rs11754455	0.81[CHB][hapmap]
rs11967108	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12190920	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12190996	0.84[EUR][1000 genomes]
rs12192847	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12193493	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12197114	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12197180	0.82[CHB][hapmap]
rs12198938	0.81[CHB][hapmap]
rs12199154	0.82[CHB][hapmap]
rs12206928	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12209691	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12212476	0.81[CHB][hapmap]
rs12213313	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12524273	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12524502	0.81[CEU][hapmap]
rs12524639	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12528712	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs13195517	0.85[CEU][hapmap]
rs13199519	0.90[CEU][hapmap]
rs13203252	0.84[CEU][hapmap]
rs13212766	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13220915	0.81[CHB][hapmap]
rs1322816	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1358997	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1358998	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1406899	0.82[CHB][hapmap]
rs1546980	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1590306	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17070580	0.95[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1923725	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2024850	0.82[CHB][hapmap]
rs2236582	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2275650	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277114	0.82[CHB][hapmap]
rs34202013	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35056702	0.89[EUR][1000 genomes]
rs36035949	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36099706	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757234	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3778475	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3778477	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3799835	0.85[CEU][hapmap]
rs3799839	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3807005	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3818934	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59056467	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59906308	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68042406	0.82[EUR][1000 genomes]
rs6911838	0.95[CEU][hapmap]
rs6920962	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs6929023	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7372	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs752262	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7754650	0.84[MKK][hapmap]
rs7755941	0.85[CHB][hapmap]
rs7773095	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7773950	0.82[CHB][hapmap]
rs9320287	0.95[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs9480933	0.94[EUR][1000 genomes]
rs9480948	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9480951	0.89[EUR][1000 genomes]
rs9480953	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs9480955	0.89[EUR][1000 genomes]
rs9480957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9487068	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9487094	0.95[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs9487095	0.89[EUR][1000 genomes]
rs9487097	0.85[EUR][1000 genomes]
rs9487098	0.86[EUR][1000 genomes]
rs9487100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9885646	0.95[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][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	nsv5435	chr6:109633035-109669127	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12528822	PPIL6	cis	cerebellum	SCAN
rs12528822	SMPD2	cis	lymphoblastoid	seeQTL
rs12528822	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs12528822	MICAL1	cis	parietal	SCAN
rs12528822	SMPD2	cis	cerebellum	SCAN
rs12528822	SMPD2	cis	parietal	SCAN
rs12528822	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs12528822	CD164	cis	parietal	SCAN
rs12528822	AKD1	cis	cerebellum	SCAN
rs12528822	PDSS2	cis	cerebellum	SCAN
rs12528822	SMPD2	cis	Whole Blood	GTEx
rs12528822	SMPD2	cis	multi-tissue	Pritchard
rs12528822	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12528822	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109644600-109675200	Weak transcription	Primary T cells from cord blood	blood
2	chr6:109645400-109662400	Weak transcription	Aorta	Aorta
3	chr6:109654000-109669400	Weak transcription	Small Intestine	intestine
4	chr6:109654200-109671000	Weak transcription	Spleen	Spleen
5	chr6:109654200-109675000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:109654200-109676200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:109654400-109668800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:109656800-109662600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:109657800-109662200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:109657800-109662200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:109657800-109671000	Weak transcription	Lung	lung
12	chr6:109658200-109663600	Weak transcription	Left Ventricle	heart
13	chr6:109658400-109665200	Weak transcription	Fetal Intestine Small	intestine
14	chr6:109658400-109669200	Weak transcription	Liver	Liver
15	chr6:109658600-109662200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:109658600-109662200	Weak transcription	Right Ventricle	heart
17	chr6:109658600-109668200	Weak transcription	Colonic Mucosa	Colon
18	chr6:109658600-109670600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:109658800-109662000	Weak transcription	Adipose Nuclei	Adipose
20	chr6:109658800-109663600	Weak transcription	Gastric	stomach
21	chr6:109658800-109663600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:109658800-109670600	Weak transcription	Right Atrium	heart
23	chr6:109658800-109677000	Weak transcription	Fetal Stomach	stomach
24	chr6:109660200-109677200	Weak transcription	Thymus	Thymus
25	chr6:109660400-109662000	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr6:109660400-109674600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:109660600-109665800	Enhancers	Fetal Muscle Leg	muscle
28	chr6:109660600-109666000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:109660800-109661600	Enhancers	Primary hematopoietic stem cells	blood
30	chr6:109660800-109666000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr6:109661000-109661600	Enhancers	Placenta	Placenta
32	chr6:109661000-109661800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:109661200-109661800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:109661200-109661800	Flanking Active TSS	K562	blood
35	chr6:109661200-109662400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr6:109661200-109665000	Weak transcription	Pancreas	Pancrea
37	chr6:109661200-109668600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr6:109661400-109661800	Enhancers	Stomach Mucosa	stomach
39	chr6:109661400-109662400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:109661400-109662600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:109661400-109662800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:109661400-109662800	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr6:109661400-109671400	Weak transcription	Fetal Thymus	thymus

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