Variant report

Variant	rs12529984
Chromosome Location	chr6:71104467-71104468
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:97)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:97 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr6:71104359-71104698	GM12891	blood:	n/a	n/a
2	PML	chr6:71104015-71105001	K562	blood:	n/a	n/a
3	NR2F2	chr6:71104200-71104843	K562	blood:	n/a	n/a
4	POLR2A	chr6:71104394-71104614	Gliobla	brain:	n/a	n/a
5	YY1	chr6:71104231-71104766	K562	blood:	n/a	n/a
6	MYC	chr6:71104233-71105424	K562	blood:	n/a	n/a
7	ZMIZ1	chr6:71104112-71104894	K562	blood:	n/a	n/a
8	GABPA	chr6:71104219-71104723	K562	blood:	n/a	n/a
9	MYC	chr6:71104199-71105181	K562	blood:	n/a	n/a
10	POLR2A	chr6:71104129-71115339	K562	blood:	n/a	n/a
11	JUND	chr6:71104221-71104888	K562	blood:	n/a	n/a
12	CEBPD	chr6:71104195-71105262	K562	blood:	n/a	n/a
13	CREB1	chr6:71104205-71104882	K562	blood:	n/a	n/a
14	TBL1XR1	chr6:71104227-71105227	K562	blood:	n/a	n/a
15	CREB1	chr6:71104108-71104982	K562	blood:	n/a	n/a
16	MYC	chr6:71104245-71105085	K562	blood:	n/a	n/a
17	MAX	chr6:71104283-71104803	K562	blood:	n/a	n/a
18	JUN	chr6:71104169-71104753	K562	blood:	n/a	n/a
19	TAF1	chr6:71104203-71104841	K562	blood:	n/a	n/a
20	STAT5A	chr6:71104123-71104863	K562	blood:	n/a	n/a
21	MYC	chr6:71104229-71105076	K562	blood:	n/a	n/a
22	HEY1	chr6:71104105-71104974	K562	blood:	n/a	n/a
23	TEAD4	chr6:71104020-71105145	K562	blood:	n/a	n/a
24	RAD21	chr6:71104218-71104519	K562	blood:	n/a	n/a
25	TBL1XR1	chr6:71104206-71105006	K562	blood:	n/a	n/a
26	MXI1	chr6:71104255-71106572	K562	blood:	n/a	n/a
27	GABPA	chr6:71104276-71104765	K562	blood:	n/a	n/a
28	E2F6	chr6:71104309-71104489	K562	blood:	n/a	n/a
29	MAX	chr6:71104222-71104855	K562	blood:	n/a	n/a
30	UBTF	chr6:71104242-71104889	K562	blood:	n/a	n/a
31	CEBPB	chr6:71104282-71104910	K562	blood:	n/a	n/a
32	POLR2A	chr6:71104156-71105579	K562	blood:	n/a	n/a
33	TAF1	chr6:71104138-71104801	K562	blood:	n/a	n/a
34	SRF	chr6:71104465-71104741	K562	blood:	n/a	n/a
35	CBX3	chr6:71104101-71104918	K562	blood:	n/a	n/a
36	CEBPB	chr6:71104373-71104664	K562	blood:	n/a	n/a
37	MYC	chr6:71104170-71105236	K562	blood:	n/a	n/a
38	CTCF	chr6:71103894-71104711	K562	blood:	n/a	n/a
39	MYC	chr6:71104363-71104828	K562	blood:	n/a	n/a
40	ELF1	chr6:71104175-71104744	K562	blood:	n/a	chr6:71104444-71104457
41	HEY1	chr6:71104135-71105482	K562	blood:	n/a	n/a
42	BCLAF1	chr6:71104202-71105526	K562	blood:	n/a	n/a
43	CTCF	chr6:71104168-71104612	K562	blood:	n/a	n/a
44	ATF1	chr6:71104145-71104785	K562	blood:	n/a	n/a
45	SIN3AK20	chr6:71104416-71104881	K562	blood:	n/a	n/a
46	STAT5A	chr6:71104455-71104833	K562	blood:	n/a	n/a
47	E2F6	chr6:71104284-71104857	K562	blood:	n/a	n/a
48	IRF1	chr6:71104179-71104782	K562	blood:	n/a	n/a
49	CEBPD	chr6:71104169-71105056	K562	blood:	n/a	n/a
50	USF1	chr6:71104245-71104772	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:71103256..71105709-chr6:71376472..71378763,2	K562	blood:
2	chr6:70931634..70934194-chr6:71104182..71105989,2	K562	blood:
3	chr6:70991053..70993906-chr6:71103584..71105214,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM135A-1	chr6:71104207-71104746	NONHSAT113439

No data

Variant related genes	Relation type
ENSG00000237643	TF binding region
ENSG00000112305	Chromatin interaction
ENSG00000112280	Chromatin interaction
ENSG00000253809	Chromatin interaction

Extended variants
information (count: 154 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10214805	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs10455706	0.87[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]
rs1048886	0.87[CEU][hapmap]
rs1075263	0.87[CEU][hapmap];0.94[EUR][1000 genomes]
rs10945230	0.93[CEU][hapmap]
rs10945231	0.93[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs11965656	0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs12197942	0.93[CEU][hapmap]
rs12197963	0.93[CEU][hapmap]
rs12200777	0.93[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs12203298	0.93[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs12209965	0.93[CEU][hapmap]
rs12216376	0.93[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs12524814	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs12525777	0.85[EUR][1000 genomes]
rs12526164	0.93[CEU][hapmap]
rs12526787	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs12526827	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12526961	0.85[EUR][1000 genomes]
rs12527634	0.87[CEU][hapmap]
rs12528385	0.85[EUR][1000 genomes]
rs12528391	0.95[EUR][1000 genomes]
rs12528866	0.82[EUR][1000 genomes]
rs12529284	0.93[CEU][hapmap]
rs12529309	0.93[CEU][hapmap]
rs12530057	0.93[CEU][hapmap]
rs12530358	0.85[EUR][1000 genomes]
rs16869156	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs16869158	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs16869168	0.85[EUR][1000 genomes]
rs16869170	0.87[CEU][hapmap];0.94[EUR][1000 genomes]
rs16869267	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs16869370	0.87[CEU][hapmap];0.84[GIH][hapmap]
rs16869371	0.93[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap]
rs16869373	0.93[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap]
rs1739338	0.87[CEU][hapmap]
rs17634272	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs17634491	0.85[EUR][1000 genomes]
rs17635446	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs17635510	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs17706748	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs17706833	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs17713105	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs17713212	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs17713547	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs2207423	0.93[CEU][hapmap]
rs2207425	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs2273210	0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2293297	0.92[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap]
rs2295200	0.87[CEU][hapmap]
rs2346889	0.87[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs2346890	0.87[CEU][hapmap]
rs2639297	0.87[CEU][hapmap];0.88[GIH][hapmap]
rs2691486	0.84[CEU][hapmap]
rs2691496	0.87[CEU][hapmap]
rs2747702	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs2842063	0.87[CEU][hapmap];0.84[GIH][hapmap]
rs3193656	0.93[CEU][hapmap]
rs3846746	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3846748	1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[EUR][1000 genomes]
rs3846750	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs3889007	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs41265349	0.92[EUR][1000 genomes]
rs4283855	0.87[CEU][hapmap]
rs4496758	0.86[CEU][hapmap]
rs4707802	0.87[EUR][1000 genomes]
rs55761717	0.85[EUR][1000 genomes]
rs55990553	0.83[EUR][1000 genomes]
rs55990831	0.85[EUR][1000 genomes]
rs56351105	0.91[EUR][1000 genomes]
rs56397968	0.92[EUR][1000 genomes]
rs58144467	0.94[EUR][1000 genomes]
rs58637377	0.85[EUR][1000 genomes]
rs59275635	0.83[EUR][1000 genomes]
rs59698166	0.85[EUR][1000 genomes]
rs6455367	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6455370	0.93[CEU][hapmap]
rs6900840	0.86[CEU][hapmap]
rs6901904	0.82[EUR][1000 genomes]
rs6902773	0.85[EUR][1000 genomes]
rs6902986	0.86[EUR][1000 genomes]
rs6906592	0.87[CEU][hapmap]
rs6911812	0.87[CEU][hapmap]
rs6911983	0.93[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap]
rs6913548	0.85[CEU][hapmap]
rs6915405	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6916974	0.93[CEU][hapmap]
rs6918393	0.80[CEU][hapmap];0.87[GIH][hapmap]
rs6923292	0.85[EUR][1000 genomes]
rs6931901	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6932470	0.95[EUR][1000 genomes]
rs6933150	0.87[CEU][hapmap]
rs6933337	0.95[EUR][1000 genomes]
rs6934660	0.93[EUR][1000 genomes]
rs6936550	0.92[EUR][1000 genomes]
rs6940416	0.84[GIH][hapmap]
rs6942012	0.93[CEU][hapmap]
rs73474910	0.93[EUR][1000 genomes]
rs73474927	0.95[EUR][1000 genomes]
rs73474934	0.95[EUR][1000 genomes]
rs73474937	0.94[EUR][1000 genomes]
rs73474966	0.84[EUR][1000 genomes]
rs73474998	0.82[EUR][1000 genomes]
rs73478819	0.82[EUR][1000 genomes]
rs73482554	0.82[EUR][1000 genomes]
rs73482557	0.82[EUR][1000 genomes]
rs73482585	0.82[EUR][1000 genomes]
rs7740873	0.93[CEU][hapmap];0.84[GIH][hapmap]
rs7741265	0.93[CEU][hapmap]
rs7742044	0.81[EUR][1000 genomes]
rs7743819	1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[EUR][1000 genomes]
rs7752409	0.87[CEU][hapmap];0.88[GIH][hapmap]
rs7753355	0.87[CEU][hapmap]
rs7756774	0.93[CEU][hapmap]
rs7757026	0.93[CEU][hapmap]
rs7759464	0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs7766075	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs7767149	0.85[EUR][1000 genomes]
rs7769582	0.87[CEU][hapmap];0.84[GIH][hapmap]
rs7775962	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs9283835	0.93[CEU][hapmap]
rs9294868	0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs9294872	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs9294874	0.87[CEU][hapmap]
rs9294876	0.93[CEU][hapmap];0.84[GIH][hapmap]
rs9446245	0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs9446246	0.80[EUR][1000 genomes]
rs9446248	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs9446267	0.93[CEU][hapmap]
rs9455092	0.87[CEU][hapmap]
rs9455093	0.81[EUR][1000 genomes]
rs9455094	0.88[EUR][1000 genomes]
rs9455097	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs9455101	0.88[EUR][1000 genomes]
rs9455104	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs9455105	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs9455113	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs9455121	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs9455132	0.87[CEU][hapmap]
rs9455139	0.82[EUR][1000 genomes]
rs9455150	0.93[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs9455151	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs9455158	0.93[CEU][hapmap];0.84[GIH][hapmap]
rs9455160	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs9455162	0.93[CEU][hapmap]
rs9455163	0.93[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1026229	chr6:71016272-71183503	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv886144	chr6:71018467-71214201	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1032876	chr6:71048428-71145166	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12529984	C10orf140	trans	cerebellum	SCAN
rs12529984	C6orf57	cis	cerebellum	SCAN
rs12529984	C6orf57	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71097600-71108000	Enhancers	Fetal Intestine Large	intestine
2	chr6:71099400-71108400	Enhancers	Fetal Intestine Small	intestine
3	chr6:71099800-71104800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:71100400-71105800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:71100400-71105800	Weak transcription	A549	lung
6	chr6:71102000-71105800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:71102200-71105000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:71103600-71122400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:71104200-71104800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:71104200-71104800	Enhancers	Colonic Mucosa	Colon
11	chr6:71104200-71104800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:71104200-71104800	Enhancers	Small Intestine	intestine
13	chr6:71104200-71105000	Enhancers	HepG2	liver
14	chr6:71104200-71105800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr6:71104200-71107200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:71104200-71108000	Enhancers	Stomach Mucosa	stomach
17	chr6:71104400-71104600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:71104400-71104600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr6:71104400-71104800	Enhancers	Esophagus	oesophagus
20	chr6:71104400-71104800	Enhancers	Placenta	Placenta
21	chr6:71104400-71104800	Flanking Active TSS	Pancreas	Pancrea
22	chr6:71104400-71107200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:71104400-71108200	Active TSS	K562	blood

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