Variant report

Variant	rs2342769
Chromosome Location	chr6:150216507-150216508
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	TBP	chr6:150216444-150216836	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:150216277-150216765	Hela-S3	cervix:	n/a	n/a
3	JUND	chr6:150216385-150218199	HCT-116	colon:	n/a	chr6:150217889-150217898 chr6:150217888-150217900 chr6:150217888-150217899 chr6:150217890-150217897 chr6:150217891-150217902 chr6:150217889-150217899 chr6:150217890-150217899
4	POLR2A	chr6:150216338-150216846	U87	brain:	n/a	n/a
5	STAT3	chr6:150216414-150216818	MCF10A-Er-Src	breast:	n/a	chr6:150216599-150216610
6	CHD1	chr6:150216356-150216844	IMR90	lung:	n/a	n/a
7	FOXA2	chr6:150216168-150216806	A549	lung:	n/a	n/a
8	POLR2A	chr6:150216178-150217814	Hela-S3	cervix:	n/a	n/a
9	FOXA2	chr6:150216097-150216760	A549	lung:	n/a	n/a
10	GTF2F1	chr6:150216436-150217513	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr6:150216452-150217510	Hela-S3	cervix:	n/a	chr6:150216677-150216694
12	EGR1	chr6:150216169-150216832	HCT-116	colon:	n/a	n/a
13	POLR2A	chr6:150216441-150216777	MCF10A-Er-Src	breast:	n/a	n/a
14	CTCF	chr6:150216500-150216650	BJ	skin:	n/a	n/a
15	POLR2A	chr6:150216330-150217490	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr6:150216460-150216610	BJ	skin:	n/a	n/a
17	STAT3	chr6:150216429-150217204	MCF10A-Er-Src	breast:	n/a	chr6:150216599-150216610
18	POLR2A	chr6:150216454-150216825	U87	brain:	n/a	n/a
19	CTCF	chr6:150216480-150216630	HFF	foreskin:	n/a	n/a
20	POLR2A	chr6:150216330-150216808	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr6:150216360-150216510	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr6:150216360-150216510	HEK293	kidney:	n/a	n/a
23	POLR2A	chr6:150216339-150217277	MCF10A-Er-Src	breast:	n/a	n/a
24	FOXP2	chr6:150216413-150216702	PFSK-1	brain:	n/a	n/a
25	SMC3	chr6:150216229-150217427	Hela-S3	cervix:	n/a	n/a
26	MAX	chr6:150216270-150217497	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr6:150216346-150217438	Hela-S3	cervix:	n/a	n/a
28	FOXA1	chr6:150216359-150216827	HepG2	liver:	n/a	n/a
29	TCF7L2	chr6:150216362-150216699	Hela-S3	cervix:	n/a	n/a
30	FOXA1	chr6:150216207-150216762	HepG2	liver:	n/a	n/a
31	FOXA1	chr6:150216257-150216833	HepG2	liver:	n/a	n/a
32	SP1	chr6:150216244-150218167	HCT-116	colon:	n/a	chr6:150218010-150218017
33	STAT3	chr6:150216427-150216900	MCF10A-Er-Src	breast:	n/a	chr6:150216599-150216610
34	RAD21	chr6:150216179-150216780	Hela-S3	cervix:	n/a	n/a
35	FOXA2	chr6:150216346-150216732	HepG2	liver:	n/a	n/a
36	CTCF	chr6:150216230-150216558	K562	blood:	n/a	n/a
37	POLR2A	chr6:150216332-150217500	U87	brain:	n/a	n/a
38	CHD2	chr6:150216354-150216744	Hela-S3	cervix:	n/a	n/a
39	FOXA1	chr6:150216341-150216776	T-47D	breast:	n/a	n/a
40	FOXA1	chr6:150216401-150216762	T-47D	breast:	n/a	n/a
41	POLR2A	chr6:150216150-150216799	HCT-116	colon:	n/a	n/a
42	FOXA1	chr6:150216274-150216727	HepG2	liver:	n/a	n/a
43	STAT3	chr6:150216419-150217283	MCF10A-Er-Src	breast:	n/a	chr6:150216599-150216610

No.	Distal block	Cell Line	Cell type
1	chr6:150185187..150186828-chr6:150215109..150217579,2	MCF-7	breast:
2	chr6:150183832..150186232-chr6:150215270..150224001,9	MCF-7	breast:
3	chr6:150212160..150213980-chr6:150214968..150218117,3	K562	blood:
4	chr12:120730015..120730787-chr6:150215970..150216651,2	Hela-S3	cervix:

Variant related genes	Relation type
RAET1E	TF binding region
ENSG00000120256	Chromatin interaction
ENSG00000268592	Chromatin interaction
ENSG00000164520	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1334510	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2095376	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2342767	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]
rs2342768	0.87[EUR][1000 genomes]
rs2342770	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]
rs3823021	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4458704	1.00[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs4869763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869764	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870116	0.92[EUR][1000 genomes]
rs6557133	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6933882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935829	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6939761	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742692	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7747435	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7747457	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753544	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7756850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7758020	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]
rs7758033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7763719	0.83[EUR][1000 genomes]
rs7763849	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]
rs7764376	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767588	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7767592	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7768626	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]
rs7768665	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7771014	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7774787	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322225	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9322228	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]
rs9371215	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9371223	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];0.98[ASN][1000 genomes]
rs9371504	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9371505	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9371533	0.92[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9371541	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9371542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9371544	0.87[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9383577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383912	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383913	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9383914	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]
rs9383921	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]
rs9383940	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9397058	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]
rs9397398	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9397420	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]
rs9397434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9397438	0.83[JPT][hapmap]
rs9478192	0.81[EUR][1000 genomes]
rs9968871	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]
rs9969044	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]
rs9986576	0.81[CEU][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	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2342769	RAET1E	cis	Esophagus Mucosa	GTEx
rs2342769	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs2342769	RP11-350J20.5	cis	Thyroid	GTEx
rs2342769	LRP11	cis	Adipose Subcutaneous	GTEx
rs2342769	RP11-350J20.9	cis	lung	GTEx
rs2342769	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs2342769	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs2342769	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs2342769	RAET1G	cis	Skin Sun Exposed Lower leg	GTEx
rs2342769	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs2342769	RAET1E	cis	Nerve Tibial	GTEx
rs2342769	RP11-350J20.9	cis	Muscle Skeletal	GTEx
rs2342769	RAET1G	cis	Thyroid	GTEx
rs2342769	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150209600-150222200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:150212800-150216600	Weak transcription	HSMM	muscle
3	chr6:150215800-150216600	Enhancers	A549	lung
4	chr6:150215800-150216600	Enhancers	NHEK	skin
5	chr6:150215800-150217200	Enhancers	NHDF-Ad	bronchial
6	chr6:150215800-150217800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
7	chr6:150215800-150217800	Enhancers	Right Ventricle	heart
8	chr6:150215800-150218200	Enhancers	Adipose Nuclei	Adipose
9	chr6:150215800-150219200	Enhancers	Stomach Mucosa	stomach
10	chr6:150216000-150216600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:150216000-150216800	Enhancers	HMEC	breast
12	chr6:150216000-150217000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr6:150216000-150217000	Enhancers	HepG2	liver
14	chr6:150216000-150217200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:150216000-150217200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr6:150216000-150217600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:150216000-150217800	Enhancers	Duodenum Mucosa	Duodenum
18	chr6:150216000-150218000	Enhancers	NHLF	lung
19	chr6:150216000-150218200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:150216000-150218200	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr6:150216000-150218200	Enhancers	Esophagus	oesophagus
22	chr6:150216000-150218200	Enhancers	Fetal Lung	lung
23	chr6:150216000-150218200	Enhancers	Ovary	ovary
24	chr6:150216000-150218200	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr6:150216000-150218200	Enhancers	Spleen	Spleen
26	chr6:150216000-150218400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:150216000-150218400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:150216000-150218400	Enhancers	Colon Smooth Muscle	Colon
29	chr6:150216000-150218600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:150216000-150218600	Enhancers	Psoas Muscle	Psoas
31	chr6:150216000-150218800	Enhancers	Fetal Stomach	stomach
32	chr6:150216000-150219000	Enhancers	Placenta	Placenta
33	chr6:150216000-150219000	Enhancers	Right Atrium	heart
34	chr6:150216000-150219200	Enhancers	Left Ventricle	heart
35	chr6:150216000-150219400	Enhancers	Lung	lung
36	chr6:150216000-150219400	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr6:150216000-150219400	Flanking Active TSS	Hela-S3	cervix
38	chr6:150216000-150222600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:150216200-150216600	Enhancers	H1 Cell Line	embryonic stem cell
40	chr6:150216200-150216600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:150216200-150216600	Flanking Active TSS	Colonic Mucosa	Colon
42	chr6:150216200-150216600	Enhancers	Pancreas	Pancrea
43	chr6:150216200-150216600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr6:150216200-150216600	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr6:150216200-150217000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:150216200-150217400	Enhancers	Fetal Intestine Small	intestine
47	chr6:150216200-150217600	Enhancers	Rectal Smooth Muscle	rectum
48	chr6:150216200-150218000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:150216200-150218000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:150216200-150218000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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