Variant report

Variant	rs9450751
Chromosome Location	chr6:88299310-88299311
allele	A/C
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	POLR2A	chr6:88299252-88300238	GM12892	blood:	n/a	n/a
2	GABPA	chr6:88299060-88300322	A549	lung:	n/a	n/a
3	POLR2A	chr6:88299262-88300228	HUVEC	blood vessel:	n/a	n/a
4	BHLHE40	chr6:88299176-88300272	K562	blood:	n/a	chr6:88299823-88299839
5	POLR2A	chr6:88298921-88300389	HepG2	liver:	n/a	n/a
6	SP1	chr6:88299222-88300222	HCT-116	colon:	n/a	chr6:88299780-88299801
7	RCOR1	chr6:88299195-88300503	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:88299102-88300725	HepG2	liver:	n/a	n/a
9	SIN3AK20	chr6:88299258-88300229	MCF-7	breast:	n/a	n/a
10	ELF1	chr6:88299218-88300205	MCF-7	breast:	n/a	n/a
11	TBP	chr6:88299270-88300279	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF1	chr6:88299295-88300271	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr6:88299191-88300155	HUVEC	blood vessel:	n/a	n/a
14	GABPA	chr6:88299246-88300373	SK-N-SH	brain:	n/a	n/a
15	REST	chr6:88299302-88300108	A549	lung:	n/a	n/a
16	IRF1	chr6:88299180-88300105	K562	blood:	n/a	chr6:88299781-88299790 chr6:88299718-88299732
17	UBTF	chr6:88299082-88299805	K562	blood:	n/a	n/a
18	POLR2A	chr6:88299300-88300227	K562	blood:	n/a	n/a
19	NR2F2	chr6:88299258-88300509	K562	blood:	n/a	chr6:88299811-88299826
20	POLR2A	chr6:88299299-88300200	PFSK-1	brain:	n/a	n/a
21	GABPA	chr6:88299019-88300460	MCF-7	breast:	n/a	n/a
22	MAX	chr6:88299235-88300293	MCF-7	breast:	n/a	n/a
23	GABPA	chr6:88299240-88300310	SK-N-SH	brain:	n/a	n/a
24	RELA	chr6:88299310-88300150	GM12891	blood:	n/a	chr6:88299844-88299853 chr6:88299844-88299853
25	SIN3AK20	chr6:88299143-88300446	MCF-7	breast:	n/a	n/a
26	GABPA	chr6:88299262-88300195	HL-60	blood:	n/a	n/a
27	KAP1	chr6:88299090-88300327	HEK293	kidney:	n/a	n/a
28	POLR2A	chr6:88299241-88300286	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr6:88299302-88300157	GM12891	blood:	n/a	n/a
30	E2F4	chr6:88299204-88300993	MCF10A-Er-Src	breast:	n/a	chr6:88299841-88299848 chr6:88299841-88299848 chr6:88299838-88299849 chr6:88299837-88299849 chr6:88299781-88299790 chr6:88299841-88299848
31	POLR2A	chr6:88299164-88300205	K562	blood:	n/a	n/a
32	TAF1	chr6:88299268-88300371	H1-hESC	embryonic stem cell:	n/a	n/a
33	PML	chr6:88299089-88300288	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:88299255-88300332	SK-N-MC	brain:	n/a	n/a
35	POLR2A	chr6:88298508-88300179	IMR90	lung:	n/a	n/a
36	HEY1	chr6:88299298-88300201	HepG2	liver:	n/a	n/a
37	RCOR1	chr6:88299203-88300315	K562	blood:	n/a	n/a
38	POLR2A	chr6:88299263-88300216	U87	brain:	n/a	n/a
39	ELF1	chr6:88299101-88300215	HCT-116	colon:	n/a	n/a
40	HA-E2F1	chr6:88299288-88300285	MCF-7	breast:	n/a	chr6:88299841-88299848 chr6:88299841-88299848 chr6:88299837-88299849 chr6:88299781-88299790 chr6:88299841-88299848
41	POLR2A	chr6:88299223-88300221	K562	blood:	n/a	n/a
42	UBTF	chr6:88299109-88300192	K562	blood:	n/a	n/a
43	POLR2A	chr6:88299144-88300431	PBDE	blood:	n/a	n/a
44	FOXA1	chr6:88299264-88299956	HepG2	liver:	n/a	n/a
45	TCF12	chr6:88299295-88300132	A549	lung:	n/a	n/a
46	MXI1	chr6:88299282-88300278	GM12878	blood:	n/a	n/a
47	POLR2A	chr6:88299212-88300280	K562	blood:	n/a	n/a
48	RAD21	chr6:88298948-88300335	IMR90	lung:	n/a	n/a
49	POLR2A	chr6:88299291-88300120	GM12878	blood:	n/a	n/a
50	MXI1	chr6:88298424-88301082	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:88274592..88276563-chr6:88297497..88299608,2	MCF-7	breast:
2	chr6:88298942..88303064-chr6:88409165..88412231,4	K562	blood:
3	chr6:88299129..88299891-chr8:92081843..92082472,2	NB4	blood:
4	chr6:88298133..88299802-chr6:88410474..88412513,2	MCF-7	breast:
5	chr6:88181710..88183852-chr6:88298759..88301128,2	K562	blood:
6	chr6:88277452..88280023-chr6:88298199..88301235,3	MCF-7	breast:

Variant related genes	Relation type
ORC3	TF binding region
ENSG00000253738	Chromatin interaction
ENSG00000155100	Chromatin interaction
ENSG00000135334	Chromatin interaction
ENSG00000146282	Chromatin interaction
ENSG00000164414	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1052623	0.94[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs1075665	0.86[EUR][1000 genomes]
rs11962148	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11965562	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs11970493	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11970696	0.90[CHB][hapmap]
rs12524205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12529993	0.90[ASN][1000 genomes]
rs12530371	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13214442	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs16879887	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs16879893	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2223877	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs2246051	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2246057	0.90[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap]
rs2268996	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap]
rs2295088	0.95[CHB][hapmap];0.82[CHD][hapmap]
rs2300898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2300899	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2300900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2300904	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs2300908	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs34513746	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3778671	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs3818057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4132446	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4354121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707378	0.91[EUR][1000 genomes]
rs4707385	0.93[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs58305152	0.90[ASN][1000 genomes]
rs6454634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6914244	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6915077	0.90[CHB][hapmap]
rs6927171	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs6928057	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs728582	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs7649	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs7761943	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9294384	0.87[EUR][1000 genomes]
rs9294385	0.85[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs9444499	0.90[CHB][hapmap]
rs9444501	0.90[CHB][hapmap]
rs9444509	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9444513	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9444514	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444516	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9444521	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444531	0.86[EUR][1000 genomes]
rs9444534	0.80[EUR][1000 genomes]
rs9450677	0.89[CHB][hapmap]
rs9450681	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs9450686	0.90[CHB][hapmap]
rs9450693	0.90[CHB][hapmap]
rs9450694	0.83[CHB][hapmap]
rs9450697	0.89[CHB][hapmap]
rs9450698	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs9450699	1.00[CHB][hapmap]
rs9450700	1.00[CHB][hapmap]
rs9450708	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9450709	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9450716	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs9450717	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs9450728	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450729	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450734	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450735	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450740	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[ASN][1000 genomes]
rs9450741	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450743	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450749	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450750	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450756	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450760	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450763	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9474	0.94[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv538354	chr6:88273858-88311606	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9450751	C6orf162	cis	parietal	SCAN
rs9450751	AKIRIN2	cis	cerebellum	SCAN
rs9450751	SLC35A1	cis	multi-tissue	Pritchard
rs9450751	DDX3Y	trans	lymphoblastoid	seeQTL
rs9450751	SLC35A1	cis	parietal	SCAN
rs9450751	C6orf162	cis	cerebellum	SCAN
rs9450751	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9450751	RPS4Y1	trans	lymphoblastoid	seeQTL
rs9450751	UTY	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88297800-88301200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:88297800-88301400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr6:88298000-88300600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:88298000-88300800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:88298000-88301000	Active TSS	HSMM	muscle
6	chr6:88298000-88301400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:88298000-88301400	Active TSS	A549	lung
8	chr6:88298200-88299400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:88298200-88299400	Flanking Active TSS	Liver	Liver
10	chr6:88298200-88299600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:88298200-88300600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:88298200-88300600	Active TSS	Colonic Mucosa	Colon
13	chr6:88298200-88300800	Active TSS	Fetal Intestine Large	intestine
14	chr6:88298200-88301000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:88298200-88301000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:88298200-88301200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr6:88298400-88299400	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr6:88298400-88299400	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr6:88298400-88299400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr6:88298400-88299400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr6:88298400-88299400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr6:88298400-88299600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:88298400-88300200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr6:88298400-88300400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:88298400-88300600	Active TSS	Fetal Stomach	stomach
26	chr6:88298400-88300600	Active TSS	Lung	lung
27	chr6:88298400-88300800	Active TSS	Fetal Muscle Trunk	muscle
28	chr6:88298400-88300800	Active TSS	Right Atrium	heart
29	chr6:88298400-88300800	Active TSS	HSMMtube	muscle
30	chr6:88298400-88301000	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr6:88298600-88299600	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr6:88298600-88300600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:88298600-88300600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:88298600-88300600	Active TSS	Ovary	ovary
35	chr6:88298600-88300600	Active TSS	Pancreas	Pancrea
36	chr6:88298600-88300600	Active TSS	HMEC	breast
37	chr6:88298600-88300600	Active TSS	K562	blood
38	chr6:88298600-88300600	Active TSS	NHLF	lung
39	chr6:88298600-88300800	Active TSS	Aorta	Aorta
40	chr6:88298600-88300800	Active TSS	Left Ventricle	heart
41	chr6:88298600-88300800	Active TSS	Psoas Muscle	Psoas
42	chr6:88298600-88301000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr6:88298600-88301000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:88298800-88299400	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr6:88298800-88300200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:88298800-88300400	Active TSS	Muscle Satellite Cultured Cells	--
47	chr6:88298800-88300400	Active TSS	Brain Anterior Caudate	brain
48	chr6:88298800-88300400	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr6:88298800-88300400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr6:88298800-88300400	Active TSS	Fetal Lung	lung

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