Variant report

Variant	rs7752238
Chromosome Location	chr6:127667069-127667070
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	POLR2A	chr6:127666729-127667153	HCT-116	colon:	n/a	n/a
2	FOSL1	chr6:127666543-127667168	HCT-116	colon:	n/a	n/a
3	POLR2A	chr6:127666812-127667089	K562	blood:	n/a	n/a
4	POLR2A	chr6:127666985-127667126	K562	blood:	n/a	n/a
5	POLR2A	chr6:127666468-127667345	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr6:127664260-127668489	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:127665440..127667332-chr6:127741973..127744614,2	MCF-7	breast:

Variant related genes	Relation type
ECHDC1	TF binding region

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1073931	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1073932	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10872312	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12215298	0.80[EUR][1000 genomes]
rs13218061	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1543432	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1964130	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2038378	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2057223	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2144742	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2144743	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2180341	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2281491	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2326567	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2875972	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3756996	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3798850	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3798852	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3798857	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4280986	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4308584	0.82[AFR][1000 genomes]
rs4448121	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4472373	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4486042	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4895821	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4895822	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4895823	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4897207	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6569477	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6569478	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6569479	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6569480	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6569482	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6569483	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6569486	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67371475	0.83[EUR][1000 genomes]
rs6900074	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6903878	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6904520	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6904630	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6904834	0.83[EUR][1000 genomes]
rs6906717	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6909703	0.82[EUR][1000 genomes]
rs6910763	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6913350	0.83[EUR][1000 genomes]
rs6913424	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6916990	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6930849	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6937287	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7449576	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7739679	0.80[ASN][1000 genomes]
rs7742161	0.83[EUR][1000 genomes]
rs7745944	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7751865	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7753913	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7756336	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7756880	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7756884	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7760652	0.83[EUR][1000 genomes]
rs7760748	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7766942	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7771923	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7773484	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7774468	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7775493	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7776136	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs877102	0.83[EUR][1000 genomes]
rs877661	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs910720	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9285459	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9285460	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9321073	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9321074	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9321076	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9321079	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9372860	0.80[ASN][1000 genomes]
rs9375492	0.80[ASN][1000 genomes]
rs9375495	0.81[EUR][1000 genomes]
rs9375499	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9375501	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9375503	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9385419	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9385422	0.81[AFR][1000 genomes]
rs9388553	0.84[EUR][1000 genomes]
rs9388554	0.83[EUR][1000 genomes]
rs9388555	0.84[EUR][1000 genomes]
rs9388561	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9388568	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9388571	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9398836	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9398837	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9398838	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9398839	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398840	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398841	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9398842	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9401950	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9401951	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9401952	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9401953	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	nsv604641	chr6:127657099-127719062	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3434083	chr6:127665998-127670132	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv3363062	chr6:127666269-127670132	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv3379735	chr6:127666283-127670349	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7752238	ECHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:127665800-127667600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:127665800-127668000	Weak transcription	A549	lung
3	chr6:127665800-127669600	Weak transcription	Gastric	stomach
4	chr6:127665800-127670000	Weak transcription	Esophagus	oesophagus
5	chr6:127665800-127670800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:127665800-127671200	Weak transcription	Right Ventricle	heart
7	chr6:127665800-127671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:127665800-127672400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:127666000-127667600	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:127666000-127668000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:127666000-127668000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:127666000-127668000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:127666000-127668000	Weak transcription	Liver	Liver
14	chr6:127666000-127668200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:127666000-127668800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:127666000-127668800	Weak transcription	Fetal Heart	heart
17	chr6:127666000-127668800	Weak transcription	Fetal Kidney	kidney
18	chr6:127666000-127669400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:127666000-127669400	Weak transcription	Fetal Intestine Small	intestine
20	chr6:127666000-127669400	Weak transcription	Small Intestine	intestine
21	chr6:127666000-127669800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr6:127666000-127670000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:127666000-127670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:127666000-127670400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:127666000-127671400	Weak transcription	Fetal Lung	lung
26	chr6:127666000-127672400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:127666000-127679200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:127666000-127704000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:127666200-127667200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:127666200-127667800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:127666200-127667800	Weak transcription	HepG2	liver
32	chr6:127666200-127668600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:127666200-127669600	Weak transcription	Adipose Nuclei	Adipose
34	chr6:127666200-127671800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:127666200-127673400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:127666200-127676800	Weak transcription	Right Atrium	heart
37	chr6:127666200-127687000	Weak transcription	HSMM	muscle
38	chr6:127666400-127667800	Weak transcription	Primary B cells from cord blood	blood
39	chr6:127666400-127668000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:127666400-127670400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:127666400-127670400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr6:127666600-127667600	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr6:127666600-127668000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:127666600-127668000	Weak transcription	Hela-S3	cervix
45	chr6:127666600-127669800	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr6:127666600-127670400	Weak transcription	Dnd41	blood
47	chr6:127666800-127668000	Weak transcription	HMEC	breast
48	chr6:127667000-127667200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:127667000-127667200	Enhancers	Lung	lung
50	chr6:127667000-127668200	Weak transcription	NHEK	skin

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