Variant report

Variant	rs10456790
Chromosome Location	chr6:16752793-16752794
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	REST	chr6:16752562-16753034	PFSK-1	brain:	n/a	n/a
2	FOS	chr6:16752551-16753118	Hela-S3	cervix:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752924 chr6:16752912-16752923
3	HDAC2	chr6:16752603-16752934	HepG2	liver:	n/a	n/a
4	FOSL2	chr6:16752599-16753307	A549	lung:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752924
5	EP300	chr6:16752761-16753096	SK-N-SH_RA	brain:	n/a	chr6:16752773-16752787 chr6:16752914-16752923 chr6:16752913-16752922
6	TAF1	chr6:16752369-16753069	PFSK-1	brain:	n/a	n/a
7	CEBPB	chr6:16752427-16753248	HCT-116	colon:	n/a	chr6:16752772-16752785 chr6:16752772-16752783 chr6:16752774-16752785
8	MAFK	chr6:16752508-16753145	Hela-S3	cervix:	n/a	chr6:16752915-16752924
9	SIN3AK20	chr6:16752712-16753109	PFSK-1	brain:	n/a	n/a
10	STAT3	chr6:16752551-16753148	MCF10A-Er-Src	breast:	n/a	chr6:16752913-16752922 chr6:16752914-16752923
11	SIN3AK20	chr6:16752735-16753077	SK-N-SH	brain:	n/a	n/a
12	STAT3	chr6:16752781-16753060	MCF10A-Er-Src	breast:	n/a	chr6:16752913-16752922 chr6:16752914-16752923
13	FOSL2	chr6:16752719-16753215	MCF-7	breast:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752924
14	POLR2A	chr6:16752063-16754269	PFSK-1	brain:	n/a	n/a
15	FOSL2	chr6:16752663-16753169	SK-N-SH	brain:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752924
16	TCF7L2	chr6:16752616-16752990	Hela-S3	cervix:	n/a	chr6:16752914-16752923
17	REST	chr6:16752659-16753057	PFSK-1	brain:	n/a	n/a
18	JUND	chr6:16752757-16753102	K562	blood:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752923 chr6:16752912-16752924
19	SMC3	chr6:16752497-16753148	Hela-S3	cervix:	n/a	n/a
20	MYC	chr6:16752697-16753105	MCF10A-Er-Src	breast:	n/a	chr6:16752913-16752922 chr6:16752914-16752923
21	SP1	chr6:16752379-16753335	HCT-116	colon:	n/a	n/a
22	FOS	chr6:16752456-16753139	MCF10A-Er-Src	breast:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752924 chr6:16752912-16752923
23	EP300	chr6:16752607-16753104	HepG2	liver:	n/a	chr6:16752773-16752787 chr6:16752914-16752923 chr6:16752913-16752922
24	BRCA1	chr6:16752666-16753174	Hela-S3	cervix:	n/a	n/a
25	REST	chr6:16752787-16752983	SK-N-SH	brain:	n/a	n/a
26	EP300	chr6:16752698-16752994	SK-N-SH_RA	brain:	n/a	chr6:16752773-16752787 chr6:16752914-16752923 chr6:16752913-16752922
27	POLR2A	chr6:16752650-16754058	HepG2	liver:	n/a	n/a
28	ZKSCAN1	chr6:16752562-16753058	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr6:16752758-16752898	ProgFib	skin:	n/a	n/a
30	SP1	chr6:16752622-16753136	A549	lung:	n/a	n/a
31	EP300	chr6:16752651-16753164	HepG2	liver:	n/a	chr6:16752773-16752787 chr6:16752914-16752923 chr6:16752913-16752922
32	JUN	chr6:16752724-16753107	HepG2	liver:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752924
33	FOSL2	chr6:16752563-16753257	SK-N-SH	brain:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752924
34	CEBPB	chr6:16752729-16753125	A549	lung:	n/a	chr6:16752772-16752785 chr6:16752772-16752783 chr6:16752774-16752785
35	USF2	chr6:16752783-16753071	Hela-S3	cervix:	n/a	n/a
36	FOXA2	chr6:16752590-16753132	HepG2	liver:	n/a	n/a
37	MXI1	chr6:16752709-16753070	Hela-S3	cervix:	n/a	n/a
38	JUN	chr6:16752267-16753229	K562	blood:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752924
39	POLR2A	chr6:16752771-16753021	MCF10A-Er-Src	breast:	n/a	n/a
40	FOSL2	chr6:16752577-16753141	HepG2	liver:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752924
41	SIN3AK20	chr6:16752616-16753086	PFSK-1	brain:	n/a	n/a
42	FOXA1	chr6:16752599-16753149	HepG2	liver:	n/a	n/a
43	EP300	chr6:16752700-16753254	A549	lung:	n/a	chr6:16752773-16752787 chr6:16752914-16752923 chr6:16752913-16752922
44	RAD21	chr6:16752787-16753079	IMR90	lung:	n/a	n/a
45	TCF12	chr6:16752504-16753312	SK-N-SH	brain:	n/a	n/a
46	FOS	chr6:16752551-16753128	MCF10A-Er-Src	breast:	n/a	chr6:16752910-16752921 chr6:16752914-16752923 chr6:16752913-16752923 chr6:16752915-16752922 chr6:16752914-16752922 chr6:16752912-16752924 chr6:16752912-16752923
47	RFX5	chr6:16752509-16753139	Hela-S3	cervix:	n/a	n/a
48	GTF2F1	chr6:16752477-16753064	Hela-S3	cervix:	n/a	n/a
49	IRF3	chr6:16752688-16753112	Hela-S3	cervix:	n/a	chr6:16752914-16752923
50	MYBL2	chr6:16752487-16753150	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:16747791..16751761-chr6:16752164..16756534,5	MCF-7	breast:

Variant related genes	Relation type
ATXN1	TF binding region
ENSG00000124788	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10434861	1.00[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10456788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456789	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10456791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10949379	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194640	0.86[CEU][hapmap];0.90[JPT][hapmap]
rs16878970	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16879003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806144	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6459484	1.00[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs6915772	0.86[EUR][1000 genomes]
rs9350015	1.00[CEU][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532022	chr6:16448152-16825567	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS 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	nsv1031423	chr6:16467215-16823725	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1015992	chr6:16469059-16846847	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538148	chr6:16469059-16846847	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10456790	ATXN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:16732200-16754800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:16737600-16759400	Weak transcription	Thymus	Thymus
3	chr6:16741200-16758200	Enhancers	Fetal Heart	heart
4	chr6:16743000-16757200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:16743000-16759600	Weak transcription	Spleen	Spleen
6	chr6:16743800-16757200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr6:16745000-16759600	Weak transcription	Placenta	Placenta
8	chr6:16746200-16758400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:16746400-16756800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:16746400-16758600	Weak transcription	Primary T cells from cord blood	blood
11	chr6:16746400-16758800	Weak transcription	Fetal Thymus	thymus
12	chr6:16746800-16758600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:16748200-16754800	Genic enhancers	HepG2	liver
14	chr6:16748200-16756800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:16748200-16757200	Weak transcription	Fetal Brain Male	brain
16	chr6:16748200-16758200	Weak transcription	Brain Germinal Matrix	brain
17	chr6:16748200-16758400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:16748400-16753200	Weak transcription	Adipose Nuclei	Adipose
19	chr6:16748400-16758000	Weak transcription	Fetal Brain Female	brain
20	chr6:16748800-16753200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:16748800-16758400	Weak transcription	Gastric	stomach
22	chr6:16748800-16758600	Weak transcription	Right Atrium	heart
23	chr6:16748800-16758800	Weak transcription	Ovary	ovary
24	chr6:16748800-16759000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:16748800-16759800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:16749200-16753400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:16749200-16758400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr6:16749600-16753600	Genic enhancers	HSMM	muscle
29	chr6:16749600-16754800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:16749800-16753600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:16749800-16754000	Genic enhancers	NHDF-Ad	bronchial
32	chr6:16750000-16753800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:16750200-16753200	Strong transcription	GM12878-XiMat	blood
34	chr6:16750200-16753800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:16750200-16758600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr6:16750400-16753600	Weak transcription	Aorta	Aorta
37	chr6:16750400-16753600	Enhancers	Osteobl	bone
38	chr6:16750400-16754600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:16750400-16758600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:16750400-16758800	Weak transcription	Esophagus	oesophagus
41	chr6:16750400-16759800	Weak transcription	Lung	lung
42	chr6:16750600-16753600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:16750600-16755200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr6:16750600-16759000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:16750800-16752800	Weak transcription	Brain Substantia Nigra	brain
46	chr6:16750800-16753400	Enhancers	HSMMtube	muscle
47	chr6:16750800-16753600	Genic enhancers	Fetal Intestine Small	intestine
48	chr6:16751000-16753000	Strong transcription	Brain Hippocampus Middle	brain
49	chr6:16751000-16756200	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr6:16751000-16756800	Enhancers	Fetal Intestine Large	intestine

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