Variant report

Variant	rs9474
Chromosome Location	chr6:88411768-88411769
allele	A/C/G/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	chr6:88411412-88412312	SK-N-SH_RA	brain:	n/a	n/a
2	MYC	chr6:88411672-88412048	K562	blood:	n/a	n/a
3	TBP	chr6:88411478-88412828	GM12878	blood:	n/a	n/a
4	CUX1	chr6:88411733-88412877	GM12878	blood:	n/a	chr6:88412683-88412694 chr6:88411863-88411872 chr6:88411863-88411872
5	YY1	chr6:88411211-88412637	SK-N-SH_RA	brain:	n/a	chr6:88411618-88411629 chr6:88411965-88411982 chr6:88411959-88411981 chr6:88411713-88411722 chr6:88411563-88411577 chr6:88411714-88411728
6	POLR2A	chr6:88411437-88412043	A549	lung:	n/a	n/a
7	MTA3	chr6:88410224-88413062	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:88411232-88412550	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr6:88410475-88412201	GM12878	blood:	n/a	n/a
10	TAF1	chr6:88411155-88412142	HepG2	liver:	n/a	n/a
11	ZMIZ1	chr6:88410462-88412439	K562	blood:	n/a	n/a
12	ELK4	chr6:88411755-88412290	HEK293	kidney:	n/a	n/a
13	SIN3AK20	chr6:88411490-88412609	MCF-7	breast:	n/a	n/a
14	TEAD4	chr6:88411558-88412042	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr6:88410439-88412331	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:88410499-88412611	NB4	blood:	n/a	n/a
17	IRF1	chr6:88411272-88412778	K562	blood:	n/a	chr6:88412258-88412275 chr6:88412253-88412273 chr6:88412260-88412277 chr6:88412219-88412229
18	TAF1	chr6:88411379-88412364	GM12891	blood:	n/a	n/a
19	CEBPB	chr6:88411747-88412075	HepG2	liver:	n/a	n/a
20	RELA	chr6:88410202-88412567	GM12891	blood:	n/a	n/a
21	EP300	chr6:88411642-88412439	HepG2	liver:	n/a	chr6:88412222-88412236 chr6:88412220-88412234 chr6:88411958-88411967 chr6:88412214-88412228
22	EGR1	chr6:88411542-88411850	GM12878	blood:	n/a	chr6:88411711-88411721 chr6:88411711-88411724 chr6:88411711-88411724 chr6:88411712-88411721 chr6:88411711-88411724
23	MBD4	chr6:88411582-88412600	HepG2	liver:	n/a	n/a
24	PAX5	chr6:88411397-88412168	GM12892	blood:	n/a	n/a
25	MYC	chr6:88411591-88412138	MCF-7	breast:	n/a	n/a
26	YY1	chr6:88410993-88412252	K562	blood:	n/a	chr6:88411618-88411629 chr6:88411965-88411982 chr6:88411959-88411981 chr6:88411713-88411722 chr6:88411563-88411577 chr6:88411714-88411728
27	ETS1	chr6:88411202-88412355	K562	blood:	n/a	chr6:88411620-88411633 chr6:88412126-88412139 chr6:88412060-88412073 chr6:88412062-88412069
28	SIN3AK20	chr6:88410510-88412536	PANC-1	pancreas:	n/a	n/a
29	FOXM1	chr6:88411372-88412504	ECC-1	luminal epithelium:	n/a	n/a
30	GABPA	chr6:88411474-88412758	MCF-7	breast:	n/a	chr6:88412019-88412030 chr6:88412019-88412033 chr6:88412021-88412030
31	POLR2A	chr6:88411698-88412418	HepG2	liver:	n/a	n/a
32	MXI1	chr6:88411711-88412495	K562	blood:	n/a	n/a
33	MYC	chr6:88411760-88411780	MCF-7	breast:	n/a	n/a
34	YY1	chr6:88411125-88412328	H1-hESC	embryonic stem cell:	n/a	chr6:88411618-88411629 chr6:88411965-88411982 chr6:88411959-88411981 chr6:88411713-88411722 chr6:88411563-88411577 chr6:88411714-88411728
35	MAX	chr6:88411446-88412618	SK-N-SH	brain:	n/a	n/a
36	CHD2	chr6:88411767-88412548	H1-hESC	embryonic stem cell:	n/a	n/a
37	CHD2	chr6:88411425-88412608	GM12878	blood:	n/a	chr6:88411688-88411698
38	MYC	chr6:88411280-88412062	MCF-7	breast:	n/a	n/a
39	ZBTB7A	chr6:88410501-88412171	ECC-1	luminal epithelium:	n/a	n/a
40	FOXM1	chr6:88411611-88412322	MCF-7	breast:	n/a	n/a
41	POLR2A	chr6:88411423-88412576	MCF-7	breast:	n/a	n/a
42	ELK1	chr6:88411409-88412562	Hela-S3	cervix:	n/a	n/a
43	GATA1	chr6:88409655-88412581	PBDE	blood:	n/a	n/a
44	YY1	chr6:88410913-88412383	GM12878	blood:	n/a	chr6:88411618-88411629 chr6:88411965-88411982 chr6:88411959-88411981 chr6:88411713-88411722 chr6:88411563-88411577 chr6:88411714-88411728
45	FOXM1	chr6:88411456-88412494	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr6:88410085-88412745	MCF10A-Er-Src	breast:	n/a	n/a
47	REST	chr6:88411719-88412129	PANC-1	pancreas:	n/a	chr6:88411792-88411810
48	POLR2A	chr6:88410074-88412408	GM12891	blood:	n/a	n/a
49	POLR2A	chr6:88411415-88412526	HUVEC	blood vessel:	n/a	n/a
50	HEY1	chr6:88411398-88412680	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:88359821..88361812-chr6:88410685..88412446,2	MCF-7	breast:
2	chr6:88408898..88411861-chr6:88430189..88432233,3	K562	blood:
3	chr6:88409661..88412134-chr6:88428970..88430720,2	MCF-7	breast:
4	chr6:88298133..88299802-chr6:88410474..88412513,2	MCF-7	breast:
5	chr6:88299553..88301559-chr6:88410382..88412634,2	MCF-7	breast:
6	chr3:137893238..137894030-chr6:88411539..88412391,2	Hela-S3	cervix:
7	chr6:88180469..88184304-chr6:88409511..88413377,7	K562	blood:
8	chr6:43737968..43738716-chr6:88411322..88411973,2	Hela-S3	cervix:
9	chr16:30960366..30961296-chr6:88411722..88412389,2	Hela-S3	cervix:
10	chr6:88180469..88184304-chr6:88409409..88413377,5	K562	blood:
11	chr6:88298942..88303064-chr6:88409165..88412231,4	K562	blood:
12	chr22:39096591..39097236-chr6:88411622..88412425,2	Hela-S3	cervix:

Variant related genes	Relation type
AKIRIN2	TF binding region
ENSG00000164414	Chromatin interaction
ENSG00000175938	Chromatin interaction
ENSG00000238628	Chromatin interaction
ENSG00000112715	Chromatin interaction
ENSG00000135336	Chromatin interaction
ENSG00000272114	Chromatin interaction
ENSG00000100221	Chromatin interaction
ENSG00000138231	Chromatin interaction
ENSG00000146282	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1052623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075665	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12530371	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs2300908	0.95[JPT][hapmap]
rs3818057	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4354121	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4707385	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4707386	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58305152	0.82[ASN][1000 genomes]
rs6454634	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs9294384	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9294385	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.96[ASN][1000 genomes]
rs9444514	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs9444531	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444534	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444536	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450740	0.80[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs9450749	0.94[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs9450750	0.94[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs9450751	0.94[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs9450756	0.94[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs9450760	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9450763	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450773	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450775	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv7941	chr6:88403555-88413595	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9474	C6orf162	cis	parietal	SCAN
rs9474	RPS4Y1	trans	lymphoblastoid	seeQTL
rs9474	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9474	KDM5D	trans	lymphoblastoid	seeQTL
rs9474	SLC35A1	cis	multi-tissue	Pritchard
rs9474	EIF1AY	trans	lymphoblastoid	seeQTL
rs9474	DDX3Y	trans	lymphoblastoid	seeQTL
rs9474	SLC35A1	cis	parietal	SCAN
rs9474	AKIRIN2	cis	cerebellum	SCAN
rs9474	UTY	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88407000-88412800	Active TSS	Thymus	Thymus
2	chr6:88407400-88412600	Active TSS	Colonic Mucosa	Colon
3	chr6:88407400-88412600	Active TSS	Ovary	ovary
4	chr6:88407400-88412800	Active TSS	Aorta	Aorta
5	chr6:88407400-88413200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:88407400-88413200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:88407400-88413200	Active TSS	Psoas Muscle	Psoas
8	chr6:88407600-88412800	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:88407600-88413000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr6:88407600-88413000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:88407600-88413000	Active TSS	HSMMtube	muscle
12	chr6:88407800-88412800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:88408000-88412200	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr6:88408000-88412600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:88408000-88412600	Active TSS	A549	lung
16	chr6:88408000-88412800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:88408000-88412800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr6:88408000-88412800	Active TSS	Fetal Intestine Large	intestine
19	chr6:88408000-88412800	Active TSS	Fetal Intestine Small	intestine
20	chr6:88408000-88412800	Active TSS	Fetal Muscle Leg	muscle
21	chr6:88408000-88413000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:88408000-88413000	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr6:88408000-88413000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:88408000-88413000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr6:88408000-88413000	Active TSS	Stomach Smooth Muscle	stomach
26	chr6:88408000-88413000	Active TSS	HMEC	breast
27	chr6:88408000-88413000	Active TSS	HSMM	muscle
28	chr6:88408000-88413000	Active TSS	NHDF-Ad	bronchial
29	chr6:88408000-88413200	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr6:88408200-88412200	Active TSS	Hela-S3	cervix
31	chr6:88408200-88412200	Active TSS	Osteobl	bone
32	chr6:88408200-88412400	Active TSS	Primary monocytes fromperipheralblood	blood
33	chr6:88408200-88412600	Active TSS	Primary T cells fromperipheralblood	blood
34	chr6:88408200-88412800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr6:88408200-88412800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:88408200-88412800	Active TSS	Placenta	Placenta
37	chr6:88408200-88413000	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr6:88408200-88413000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:88408200-88413000	Active TSS	NHLF	lung
40	chr6:88408200-88413200	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr6:88408200-88413200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:88408400-88412400	Active TSS	Duodenum Mucosa	Duodenum
43	chr6:88408400-88412400	Active TSS	Fetal Lung	lung
44	chr6:88408400-88412400	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr6:88408400-88412400	Active TSS	NH-A	brain
46	chr6:88408400-88412600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:88408400-88412600	Active TSS	Liver	Liver
48	chr6:88408400-88412600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr6:88408400-88412800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:88408400-88412800	Active TSS	Fetal Stomach	stomach

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