Variant report

Variant	rs6907825
Chromosome Location	chr6:88102822-88102823
allele	C/T
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	CTCF	chr6:88102780-88102930	HAc	cerebellar:	n/a	n/a
2	RAD21	chr6:88102696-88103103	H1-hESC	embryonic stem cell:	n/a	chr6:88102935-88102954
3	RAD21	chr6:88102387-88103836	SK-N-SH	brain:	n/a	chr6:88102935-88102954
4	CTCF	chr6:88102720-88102870	HAc	cerebellar:	n/a	n/a
5	RAD21	chr6:88102736-88103186	ECC-1	luminal epithelium:	n/a	chr6:88102935-88102954
6	RAD21	chr6:88102694-88103342	MCF-7	breast:	n/a	chr6:88102935-88102954
7	CTCF	chr6:88102800-88103071	Pancreas_OC	pancreas:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
8	RAD21	chr6:88102711-88103148	A549	lung:	n/a	chr6:88102935-88102954
9	CTCF	chr6:88102729-88103165	IMR90	lung:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
10	CTCF	chr6:88102770-88103196	MCF-7	breast:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
11	TBL1XR1	chr6:88102775-88103005	K562	blood:	n/a	n/a
12	CHD2	chr6:88102757-88103104	GM12878	blood:	n/a	n/a
13	RAD21	chr6:88102694-88103244	H1-hESC	embryonic stem cell:	n/a	chr6:88102935-88102954
14	RAD21	chr6:88102761-88103159	H1-hESC	embryonic stem cell:	n/a	chr6:88102935-88102954
15	CTCF	chr6:88102798-88103033	A549	lung:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
16	CTCF	chr6:88102760-88102910	HFF-Myc	foreskin:	n/a	n/a
17	E2F4	chr6:88102795-88103113	MCF10A-Er-Src	breast:	n/a	n/a
18	SMC3	chr6:88102766-88103157	HepG2	liver:	n/a	chr6:88102936-88102950
19	CTCF	chr6:88102773-88103103	Spleen_OC	spleen:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
20	SMC3	chr6:88102486-88103369	SK-N-SH	brain:	n/a	chr6:88102936-88102950
21	RAD21	chr6:88102742-88103161	HepG2	liver:	n/a	chr6:88102935-88102954
22	ZNF143	chr6:88102799-88103115	K562	blood:	n/a	n/a
23	CTCF	chr6:88102792-88103110	HUVEC	blood vessel:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
24	RAD21	chr6:88102734-88103131	SK-N-SH_RA	brain:	n/a	chr6:88102935-88102954
25	CTCF	chr6:88102718-88103201	GM12878	blood:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
26	ZNF143	chr6:88102808-88103076	H1-hESC	embryonic stem cell:	n/a	n/a
27	RAD21	chr6:88102668-88103261	HCT-116	colon:	n/a	chr6:88102935-88102954
28	CTCF	chr6:88102705-88103141	A549	lung:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
29	SMC3	chr6:88102810-88103108	K562	blood:	n/a	chr6:88102936-88102950
30	CTCF	chr6:88102811-88103078	GM10266	blood:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
31	CTCF	chr6:88102820-88103069	Hela-S3	cervix:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
32	CTCF	chr6:88102320-88103487	SK-N-SH	brain:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
33	RAD21	chr6:88102781-88103180	ECC-1	luminal epithelium:	n/a	chr6:88102935-88102954
34	RAD21	chr6:88102652-88103210	IMR90	lung:	n/a	chr6:88102935-88102954
35	CTCF	chr6:88102800-88102950	HCM	heart:	n/a	n/a
36	WRNIP1	chr6:88102728-88103045	GM12878	blood:	n/a	n/a
37	CTCF	chr6:88102806-88103028	A549	lung:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
38	RAD21	chr6:88102717-88103153	SK-N-SH_RA	brain:	n/a	chr6:88102935-88102954
39	CTCF	chr6:88102784-88103079	SK-N-SH_RA	brain:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
40	CTCF	chr6:88102645-88103146	K562	blood:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
41	CTCF	chr6:88102766-88103087	A549	lung:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
42	CTCF	chr6:88102561-88103379	A549	lung:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
43	CTCF	chr6:88102821-88103029	LNCaP	prostate:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
44	CTCF	chr6:88102751-88103089	H1-hESC	embryonic stem cell:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
45	RAD21	chr6:88102774-88103140	GM12878	blood:	n/a	chr6:88102935-88102954
46	RAD21	chr6:88102725-88103181	Hela-S3	cervix:	n/a	chr6:88102935-88102954
47	SMC3	chr6:88102747-88103218	Hela-S3	cervix:	n/a	chr6:88102936-88102950
48	RAD21	chr6:88102722-88103354	MCF-7	breast:	n/a	chr6:88102935-88102954
49	RAD21	chr6:88102724-88103222	A549	lung:	n/a	chr6:88102935-88102954
50	CTCF	chr6:88102684-88103175	HCT-116	colon:	n/a	chr6:88102936-88102957 chr6:88102934-88102952

No.	Distal block	Cell Line	Cell type
1	chr6:88093882..88098127-chr6:88101103..88103625,3	MCF-7	breast:
2	chr6:88101491..88103875-chr6:88115341..88119071,3	MCF-7	breast:
3	chr6:88096108..88099056-chr6:88101308..88104420,3	K562	blood:
4	chr6:88102807..88103317-chr6:88181708..88182387,2	K562	blood:

Variant related genes	Relation type
C6orf164	TF binding region
ENSG00000213204	Chromatin interaction
ENSG00000272514	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1051550	0.85[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11964198	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11964212	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11964237	0.89[ASW][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.90[ASN][1000 genomes]
rs11966859	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1203156	0.83[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap]
rs12529410	0.89[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12529423	0.89[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12661245	0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12663865	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211410	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13211836	0.90[ASN][1000 genomes]
rs13217485	0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs242291	0.83[CEU][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs34977536	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35332886	0.89[ASN][1000 genomes]
rs3736740	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4329082	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4707365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707367	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707368	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707369	0.97[ASN][1000 genomes]
rs4707370	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4707371	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4707372	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs5009694	0.89[ASN][1000 genomes]
rs6454611	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6454612	0.85[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6454613	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6454614	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6454615	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6454616	0.89[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs6454617	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6454618	0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap]
rs6454621	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6454622	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6454623	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs6454624	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6454625	0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap]
rs6454626	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs6899561	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6900397	0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6906433	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6909168	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6910429	0.89[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6912282	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6912300	0.89[ASN][1000 genomes]
rs6912442	0.84[ASN][1000 genomes]
rs6912875	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6915562	0.89[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs6919775	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6920937	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6930072	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6940716	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7744338	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7744793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7746469	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7749047	0.85[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7749162	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7753821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7760108	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7761462	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7764266	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7764963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7766462	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7767220	0.84[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7773262	0.81[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7773804	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs926946	0.85[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9294378	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9342112	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9344708	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9353484	0.85[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9353486	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9353487	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9353488	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9362428	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9444493	0.95[ASN][1000 genomes]
rs9444494	0.91[ASN][1000 genomes]
rs9444495	0.93[ASN][1000 genomes]
rs9444496	0.91[ASN][1000 genomes]
rs9450672	1.00[JPT][hapmap]
rs9450674	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9450675	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9450676	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9450682	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6907825	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs6907825	C6orf162	cis	cerebellum	SCAN
rs6907825	C6orf164	cis	Muscle Skeletal	GTEx
rs6907825	C6orf162	cis	parietal	SCAN
rs6907825	C6orf164	cis	lung	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88040600-88116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:88054800-88110200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:88094800-88103400	Weak transcription	K562	blood
4	chr6:88102400-88103200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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