Variant report

Variant	rs9322228
Chromosome Location	chr6:150209309-150209310
allele	C/G
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	CEBPB	chr6:150209285-150209620	MCF-7	breast:	n/a	chr6:150209470-150209481
2	RCOR1	chr6:150209195-150209597	Hela-S3	cervix:	n/a	n/a
3	MAZ	chr6:150209263-150209670	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr6:150209235-150209665	A549	lung:	n/a	chr6:150209470-150209481
5	STAT3	chr6:150209172-150209608	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr6:150209222-150209652	A549	lung:	n/a	chr6:150209470-150209481
7	NR2F2	chr6:150209186-150209755	MCF-7	breast:	n/a	n/a
8	EP300	chr6:150209208-150209608	Hela-S3	cervix:	n/a	chr6:150209471-150209485
9	SMARCC1	chr6:150208250-150211123	Hela-S3	cervix:	n/a	chr6:150208765-150208774
10	FOS	chr6:150209299-150209589	MCF10A-Er-Src	breast:	n/a	n/a
11	MAX	chr6:150209242-150210893	Hela-S3	cervix:	n/a	n/a
12	SP1	chr6:150209119-150209713	A549	lung:	n/a	n/a
13	NR3C1	chr6:150209214-150209630	A549	lung:	n/a	chr6:150209327-150209334
14	FOXA2	chr6:150209143-150209620	A549	lung:	n/a	n/a
15	NR2F2	chr6:150209101-150209755	MCF-7	breast:	n/a	n/a
16	CEBPB	chr6:150209208-150210929	Hela-S3	cervix:	n/a	chr6:150209470-150209481
17	FOXA2	chr6:150209142-150209707	A549	lung:	n/a	n/a
18	EP300	chr6:150209091-150209738	A549	lung:	n/a	chr6:150209471-150209485
19	NR3C1	chr6:150209245-150209629	A549	lung:	n/a	chr6:150209327-150209334
20	USF2	chr6:150209204-150210912	Hela-S3	cervix:	n/a	chr6:150209928-150209939
21	POLR2A	chr6:150208491-150209777	Hela-S3	cervix:	n/a	n/a
22	SP1	chr6:150209173-150209782	A549	lung:	n/a	n/a
23	RAD21	chr6:150209229-150209572	Hela-S3	cervix:	n/a	n/a
24	EP300	chr6:150209031-150209842	A549	lung:	n/a	chr6:150209471-150209485
25	CEBPB	chr6:150209201-150209787	A549	lung:	n/a	chr6:150209470-150209481
26	TCF12	chr6:150209156-150209598	A549	lung:	n/a	n/a
27	NR3C1	chr6:150209208-150209608	A549	lung:	n/a	chr6:150209327-150209334
28	MAX	chr6:150209244-150209711	A549	lung:	n/a	n/a
29	POLR2A	chr6:150208138-150210950	Hela-S3	cervix:	n/a	n/a
30	TFAP2C	chr6:150209215-150210815	Hela-S3	cervix:	n/a	n/a
31	MYC	chr6:150209165-150210248	MCF10A-Er-Src	breast:	n/a	n/a
32	TCF12	chr6:150208318-150209752	A549	lung:	n/a	n/a
33	ZKSCAN1	chr6:150209259-150209666	Hela-S3	cervix:	n/a	n/a
34	RFX5	chr6:150209226-150209620	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr6:150209169-150209649	Hela-S3	cervix:	n/a	n/a
36	CEBPB	chr6:150209144-150209783	MCF-7	breast:	n/a	chr6:150209470-150209481
37	MAX	chr6:150209156-150209812	A549	lung:	n/a	n/a
38	MYC	chr6:150209194-150210261	MCF10A-Er-Src	breast:	n/a	n/a
39	CEBPB	chr6:150209303-150209607	IMR90	lung:	n/a	chr6:150209470-150209481
40	POLR2A	chr6:150208350-150212272	Hela-S3	cervix:	n/a	n/a
41	CREB1	chr6:150209224-150209599	A549	lung:	n/a	n/a
42	FOSL2	chr6:150209178-150209764	A549	lung:	n/a	n/a
43	STAT3	chr6:150209299-150209604	Hela-S3	cervix:	n/a	n/a
44	MXI1	chr6:150209237-150211154	Hela-S3	cervix:	n/a	n/a
45	JUND	chr6:150209274-150209588	A549	lung:	n/a	n/a
46	POLR2A	chr6:150208398-150212270	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr6:150209300-150209632	MCF10A-Er-Src	breast:	n/a	n/a
48	CHD2	chr6:150209233-150209643	Hela-S3	cervix:	n/a	n/a
49	JUND	chr6:150209156-150209642	A549	lung:	n/a	n/a
50	POLR2A	chr6:150209171-150209715	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:150182126..150185111-chr6:150208101..150209742,2	K562	blood:
2	chr6:150201367..150203467-chr6:150207974..150210289,2	MCF-7	breast:
3	chr6:150182126..150186554-chr6:150208101..150210542,3	K562	blood:
4	chr6:150183161..150188305-chr6:150206346..150214162,9	MCF-7	breast:
5	chr6:150208190..150211087-chr6:150219720..150221224,2	MCF-7	breast:
6	chr6:150182396..150187721-chr6:150207302..150210632,6	MCF-7	breast:
7	chr6:150200712..150203416-chr6:150207860..150210756,3	MCF-7	breast:
8	chr6:150208849..150210452-chr6:150245274..150246868,2	MCF-7	breast:

Variant related genes	Relation type
RAET1E-AS1	TF binding region
ENSG00000120256	Chromatin interaction
ENSG00000217733	Chromatin interaction
ENSG00000268592	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1334510	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2095376	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2342767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2342768	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2342769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2342770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3823021	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4458704	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4869763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4870116	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6557133	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6925151	0.93[YRI][hapmap]
rs6933882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935829	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6939761	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7740145	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7742692	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7742993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744821	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7747435	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7747457	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7753544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757972	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763719	0.84[EUR][1000 genomes]
rs7763849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7767588	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7767592	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7768626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768665	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771014	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7774787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322225	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9371215	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9371223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9371504	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9371505	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9371533	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9371541	0.91[ASN][1000 genomes]
rs9371542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9371544	0.88[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9383577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383584	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383912	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383913	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383940	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9397058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9397398	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9397420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9397434	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9397438	0.85[JPT][hapmap]
rs9478192	0.81[EUR][1000 genomes]
rs9968871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986576	0.81[CEU][hapmap]

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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs9322228	RP11-350J20.5	cis	Adipose Subcutaneous	GTEx
rs9322228	RAET1G	cis	Artery Tibial	GTEx
rs9322228	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs9322228	RAET1G	cis	Esophagus Mucosa	GTEx
rs9322228	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9322228	LRP11	cis	Adipose Subcutaneous	GTEx
rs9322228	RAET1G	cis	Thyroid	GTEx
rs9322228	RAET1E	cis	Nerve Tibial	GTEx
rs9322228	RP11-350J20.5	cis	Thyroid	GTEx
rs9322228	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs9322228	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs9322228	RP11-350J20.5	cis	Artery Tibial	GTEx
rs9322228	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs9322228	RP11-350J20.5	cis	lung	GTEx
rs9322228	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9322228	RP11-350J20.9	cis	lung	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150205000-150210400	Enhancers	HMEC	breast
2	chr6:150205600-150216000	Weak transcription	Right Atrium	heart
3	chr6:150205800-150210200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:150205800-150216000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:150206000-150216000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:150206600-150211600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:150207800-150210600	Enhancers	NHDF-Ad	bronchial
8	chr6:150208000-150210600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:150208000-150210600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:150208000-150210800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:150208000-150211800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:150208200-150210200	Enhancers	Esophagus	oesophagus
13	chr6:150208200-150210400	Enhancers	Fetal Intestine Small	intestine
14	chr6:150208200-150210400	Enhancers	NHLF	lung
15	chr6:150208200-150210400	Enhancers	Osteobl	bone
16	chr6:150208200-150210600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr6:150208200-150210600	Enhancers	Fetal Intestine Large	intestine
18	chr6:150208400-150210400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:150208400-150211400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:150208400-150211600	Weak transcription	Placenta	Placenta
21	chr6:150208400-150212600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr6:150208400-150212600	Flanking Active TSS	Hela-S3	cervix
23	chr6:150208600-150211400	Enhancers	HSMMtube	muscle
24	chr6:150208800-150209600	Enhancers	Adipose Nuclei	Adipose
25	chr6:150208800-150210000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:150209000-150209600	Enhancers	Duodenum Mucosa	Duodenum
27	chr6:150209000-150209600	Bivalent Enhancer	HepG2	liver
28	chr6:150209000-150209600	Enhancers	NHEK	skin
29	chr6:150209200-150210400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:150209200-150210400	Enhancers	HSMM	muscle
31	chr6:150209200-150212200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr6:150209200-150212800	Enhancers	A549	lung

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