Variant report

Variant	rs9398841
Chromosome Location	chr6:127670134-127670135
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:127668521..127671464-chr6:127672769..127675041,2	MCF-7	breast:
2	chr6:127669193..127671594-chr6:127672805..127674451,2	MCF-7	breast:
3	chr6:127587591..127589201-chr6:127668421..127670620,2	K562	blood:

Variant related genes	Relation type
ENSG00000118518	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1073931	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1073932	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10872312	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12215298	0.80[EUR][1000 genomes]
rs13218061	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1543432	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1964130	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2038378	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2057223	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2144742	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2144743	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2180341	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2281491	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2326567	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3756996	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3798850	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3798852	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3798857	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4280986	0.82[EUR][1000 genomes]
rs4308584	0.82[AFR][1000 genomes]
rs4448121	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4472373	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4486042	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4895821	0.88[EUR][1000 genomes]
rs4895822	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4895823	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4897207	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569477	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569478	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569479	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569480	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569482	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569483	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6569486	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67371475	0.81[EUR][1000 genomes]
rs6900074	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6903878	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6904520	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6904630	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6904834	0.80[EUR][1000 genomes]
rs6906717	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6910763	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6913350	0.81[EUR][1000 genomes]
rs6913424	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6916990	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6930849	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6937287	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7449576	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7742161	0.81[EUR][1000 genomes]
rs7745944	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7751865	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7752238	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7753913	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7756336	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7756880	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7756884	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7760652	0.81[EUR][1000 genomes]
rs7760748	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7766942	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7771923	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7773484	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7774468	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7775493	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7776136	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs877102	0.81[EUR][1000 genomes]
rs877661	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs910720	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9285459	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9285460	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9321073	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9321074	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9321076	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9321079	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9375499	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9375501	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9375503	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9385419	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9385422	0.80[AFR][1000 genomes]
rs9388553	0.82[EUR][1000 genomes]
rs9388554	0.81[EUR][1000 genomes]
rs9388555	0.82[EUR][1000 genomes]
rs9388561	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9388568	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9388571	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9398836	0.88[EUR][1000 genomes]
rs9398837	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398838	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398839	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9398840	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9398842	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9401950	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9401951	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9401952	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9401953	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	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	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
3	nsv965762	chr6:127669294-127698325	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9398841	ECHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:127665800-127670800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr6:127665800-127671200	Weak transcription	Right Ventricle	heart
3	chr6:127665800-127671800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:127665800-127672400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:127666000-127670400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:127666000-127671400	Weak transcription	Fetal Lung	lung
7	chr6:127666000-127672400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:127666000-127679200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:127666000-127704000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:127666200-127671800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:127666200-127673400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:127666200-127676800	Weak transcription	Right Atrium	heart
13	chr6:127666200-127687000	Weak transcription	HSMM	muscle
14	chr6:127666400-127670400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:127666400-127670400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:127666600-127670400	Weak transcription	Dnd41	blood
17	chr6:127667000-127671200	Weak transcription	K562	blood
18	chr6:127667200-127670600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:127667600-127676200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:127668000-127673400	Weak transcription	Primary B cells from cord blood	blood
21	chr6:127668800-127675800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:127669400-127670200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:127669400-127670200	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr6:127669400-127670800	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr6:127669400-127671800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:127669600-127670600	Enhancers	Lung	lung
27	chr6:127669800-127670800	ZNF genes & repeats	Fetal Muscle Leg	muscle
28	chr6:127669800-127673200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr6:127670000-127670600	ZNF genes & repeats	Esophagus	oesophagus
30	chr6:127670000-127670800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:127670000-127672000	Weak transcription	Gastric	stomach

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