Variant report

Variant	rs2342768
Chromosome Location	chr6:150209828-150209829
allele	A/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	POLR2A	chr6:150209766-150210253	Hela-S3	cervix:	n/a	n/a
2	SMARCC1	chr6:150208250-150211123	Hela-S3	cervix:	n/a	chr6:150208765-150208774
3	MAX	chr6:150209242-150210893	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr6:150209208-150210929	Hela-S3	cervix:	n/a	chr6:150209470-150209481
5	POLR2A	chr6:150209339-150210780	MCF10A-Er-Src	breast:	n/a	n/a
6	USF2	chr6:150209204-150210912	Hela-S3	cervix:	n/a	chr6:150209928-150209939
7	EP300	chr6:150209031-150209842	A549	lung:	n/a	chr6:150209471-150209485
8	POLR2A	chr6:150208138-150210950	Hela-S3	cervix:	n/a	n/a
9	TFAP2C	chr6:150209215-150210815	Hela-S3	cervix:	n/a	n/a
10	MYC	chr6:150209165-150210248	MCF10A-Er-Src	breast:	n/a	n/a
11	MYC	chr6:150209194-150210261	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr6:150208350-150212272	Hela-S3	cervix:	n/a	n/a
13	MXI1	chr6:150209237-150211154	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr6:150208398-150212270	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr6:150209820-150210230	MCF10A-Er-Src	breast:	n/a	n/a
16	TCF7L2	chr6:150208360-150211113	Hela-S3	cervix:	n/a	n/a
17	SMC3	chr6:150209264-150210884	Hela-S3	cervix:	n/a	n/a
18	TBP	chr6:150209194-150210904	Hela-S3	cervix:	n/a	n/a
19	GTF2F1	chr6:150209210-150210886	Hela-S3	cervix:	n/a	n/a

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

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

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1334510	0.84[EUR][1000 genomes]
rs2095376	0.81[EUR][1000 genomes]
rs2342767	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2342769	0.87[EUR][1000 genomes]
rs2342770	0.87[EUR][1000 genomes]
rs3823021	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4458704	0.82[EUR][1000 genomes]
rs4869763	0.87[EUR][1000 genomes]
rs4869764	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4870116	0.80[EUR][1000 genomes]
rs6557133	0.82[EUR][1000 genomes]
rs6933882	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6935829	0.87[EUR][1000 genomes]
rs6939761	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7740145	0.87[EUR][1000 genomes]
rs7742692	0.87[EUR][1000 genomes]
rs7742993	0.86[EUR][1000 genomes]
rs7744821	0.87[EUR][1000 genomes]
rs7747435	0.83[EUR][1000 genomes]
rs7747457	0.87[EUR][1000 genomes]
rs7753544	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7756850	0.87[EUR][1000 genomes]
rs7757972	0.87[EUR][1000 genomes]
rs7757984	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7758020	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7758033	0.86[EUR][1000 genomes]
rs7763849	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7764376	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7767588	0.85[EUR][1000 genomes]
rs7767592	0.85[EUR][1000 genomes]
rs7768626	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7768665	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7769118	0.85[EUR][1000 genomes]
rs7771014	0.82[EUR][1000 genomes]
rs7774787	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9322228	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9371215	0.82[EUR][1000 genomes]
rs9371223	0.86[EUR][1000 genomes]
rs9371533	0.84[EUR][1000 genomes]
rs9371542	0.86[EUR][1000 genomes]
rs9371544	0.87[EUR][1000 genomes]
rs9383577	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9383584	0.87[EUR][1000 genomes]
rs9383912	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9383913	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9383914	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9383921	0.86[EUR][1000 genomes]
rs9383940	0.84[EUR][1000 genomes]
rs9397058	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9397398	0.82[EUR][1000 genomes]
rs9397420	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9397434	0.87[EUR][1000 genomes]
rs9968871	0.85[EUR][1000 genomes]
rs9969044	0.85[EUR][1000 genomes]

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	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
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	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
rs2342768	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs2342768	NUP43	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 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	chr6:150208800-150210000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:150209200-150210400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:150209200-150210400	Enhancers	HSMM	muscle
27	chr6:150209200-150212200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr6:150209200-150212800	Enhancers	A549	lung
29	chr6:150209400-150210200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:150209400-150211000	Enhancers	Psoas Muscle	Psoas
31	chr6:150209600-150215800	Weak transcription	Adipose Nuclei	Adipose
32	chr6:150209600-150216000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:150209600-150222200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:150209800-150210200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:150209800-150210400	Enhancers	NHEK	skin

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