Variant report

Variant	rs6912282
Chromosome Location	chr6:88103000-88103001
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	RAD21	chr6:88102696-88103103	H1-hESC	embryonic stem cell:	n/a	chr6:88102935-88102954
2	RAD21	chr6:88102387-88103836	SK-N-SH	brain:	n/a	chr6:88102935-88102954
3	CTCF	chr6:88102920-88103070	NHDF-neo	bronchial:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
4	RAD21	chr6:88102736-88103186	ECC-1	luminal epithelium:	n/a	chr6:88102935-88102954
5	CTCF	chr6:88102960-88103110	A549	lung:	n/a	n/a
6	CTCF	chr6:88102842-88103069	HepG2	liver:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
7	CTCF	chr6:88102860-88103010	GM12801	blood:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
8	CTCF	chr6:88102860-88103010	Caco-2	colon:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
9	RAD21	chr6:88102694-88103342	MCF-7	breast:	n/a	chr6:88102935-88102954
10	CTCF	chr6:88102920-88103070	HPAF	blood vessel:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
11	CTCF	chr6:88102800-88103071	Pancreas_OC	pancreas:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
12	CTCF	chr6:88102920-88103070	HEK293	kidney:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
13	CTCF	chr6:88102843-88103042	MCF-7	breast:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
14	FOS	chr6:88102960-88103029	MCF10A-Er-Src	breast:	n/a	n/a
15	CTCF	chr6:88102940-88103090	NHLF	lung:	n/a	n/a
16	RAD21	chr6:88102711-88103148	A549	lung:	n/a	chr6:88102935-88102954
17	CTCF	chr6:88102860-88103010	HPF	lung:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
18	CTCF	chr6:88102900-88103050	GM12864	blood:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
19	CTCF	chr6:88102920-88103070	GM12873	blood:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
20	CTCF	chr6:88102729-88103165	IMR90	lung:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
21	CTCF	chr6:88102770-88103196	MCF-7	breast:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
22	CTCF	chr6:88102880-88103030	HRPEpiC	eye:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
23	TBL1XR1	chr6:88102775-88103005	K562	blood:	n/a	n/a
24	CHD2	chr6:88102757-88103104	GM12878	blood:	n/a	n/a
25	RAD21	chr6:88102694-88103244	H1-hESC	embryonic stem cell:	n/a	chr6:88102935-88102954
26	RAD21	chr6:88102761-88103159	H1-hESC	embryonic stem cell:	n/a	chr6:88102935-88102954
27	CTCF	chr6:88102920-88103070	HCFaa	heart:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
28	CTCF	chr6:88102860-88103010	HCPEpiC	choroid plexus:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
29	CTCF	chr6:88102880-88103030	HA-sp	spinal cord:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
30	CTCF	chr6:88102798-88103033	A549	lung:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
31	CTCF	chr6:88102920-88103070	AG09319	gingival:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
32	CTCF	chr6:88102854-88103033	ProgFib	skin:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
33	CTCF	chr6:88102940-88103090	NHEK	skin:	n/a	n/a
34	E2F4	chr6:88102795-88103113	MCF10A-Er-Src	breast:	n/a	n/a
35	SMC3	chr6:88102766-88103157	HepG2	liver:	n/a	chr6:88102936-88102950
36	CTCF	chr6:88102839-88103042	HepG2	liver:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
37	CTCF	chr6:88102773-88103103	Spleen_OC	spleen:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
38	SMC3	chr6:88102486-88103369	SK-N-SH	brain:	n/a	chr6:88102936-88102950
39	RAD21	chr6:88102742-88103161	HepG2	liver:	n/a	chr6:88102935-88102954
40	ZNF143	chr6:88102799-88103115	K562	blood:	n/a	n/a
41	CTCF	chr6:88102792-88103110	HUVEC	blood vessel:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
42	CTCF	chr6:88102940-88103090	K562	blood:	n/a	n/a
43	RAD21	chr6:88102734-88103131	SK-N-SH_RA	brain:	n/a	chr6:88102935-88102954
44	RFX5	chr6:88102833-88103158	K562	blood:	n/a	n/a
45	CTCF	chr6:88102718-88103201	GM12878	blood:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
46	RAD21	chr6:88102839-88103062	K562	blood:	n/a	chr6:88102935-88102954
47	EBF1	chr6:88102862-88103093	GM12878	blood:	n/a	n/a
48	ZNF143	chr6:88102808-88103076	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr6:88102880-88103030	MCF-7	breast:	n/a	chr6:88102936-88102957 chr6:88102934-88102952
50	CTCF	chr6:88102853-88103028	LNCaP	prostate:	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
ENSG00000272514	Chromatin interaction
ENSG00000213204	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1051550	0.93[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11964198	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11964212	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11964237	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11966859	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1203156	0.92[JPT][hapmap]
rs12529410	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12529423	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12661245	0.81[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12663865	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13211410	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13211836	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13217485	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1884320	0.80[AMR][1000 genomes]
rs242291	0.92[JPT][hapmap]
rs34977536	0.83[ASN][1000 genomes]
rs35332886	0.88[ASN][1000 genomes]
rs3736740	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4329082	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4707365	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4707367	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707368	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707369	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4707370	0.92[ASN][1000 genomes]
rs4707371	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4707372	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs5009694	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6454610	0.81[AFR][1000 genomes]
rs6454611	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6454612	0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6454613	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6454614	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6454615	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6454616	1.00[JPT][hapmap]
rs6454617	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6454618	1.00[JPT][hapmap]
rs6454621	0.88[ASN][1000 genomes]
rs6454622	1.00[JPT][hapmap]
rs6454623	1.00[JPT][hapmap]
rs6454624	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6454625	1.00[JPT][hapmap]
rs6454626	1.00[JPT][hapmap]
rs6899561	0.90[ASN][1000 genomes]
rs6900397	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6906433	0.90[ASN][1000 genomes]
rs6907825	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]
rs6909168	1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6910429	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6912300	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6912442	0.83[ASN][1000 genomes]
rs6912875	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6915562	1.00[JPT][hapmap]
rs6919775	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6920937	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6930072	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6940716	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7744338	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7744793	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7746469	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7746876	0.80[AMR][1000 genomes]
rs7749047	0.93[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7749162	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7753821	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7760108	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7761462	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7764266	0.94[ASN][1000 genomes]
rs7764963	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7766462	1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7767220	0.93[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7773262	0.84[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7773804	1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs926946	0.93[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9294378	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9342112	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344708	1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9353484	0.93[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9353486	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9353487	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9353488	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9362428	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9444493	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9444494	0.90[ASN][1000 genomes]
rs9444495	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9444496	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9450672	1.00[JPT][hapmap]
rs9450674	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9450675	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9450676	1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9450682	1.00[JPT][hapmap];0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6912282	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs6912282	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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