Variant report

Variant	rs9375501
Chromosome Location	chr6:127652539-127652540
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	chr6:127651713-127655829	K562	blood:	n/a	n/a
2	SPI1	chr6:127652474-127652721	K562	blood:	n/a	chr6:127652591-127652600
3	SPI1	chr6:127652459-127652701	GM12891	blood:	n/a	chr6:127652591-127652600
4	SPI1	chr6:127652387-127652864	HL-60	blood:	n/a	chr6:127652591-127652600
5	SPI1	chr6:127652474-127652707	K562	blood:	n/a	chr6:127652591-127652600
6	SPI1	chr6:127652418-127652690	GM12891	blood:	n/a	chr6:127652591-127652600

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:127652338..127654824-chr6:127662832..127665222,5	MCF-7	breast:
2	chr6:127646597..127649451-chr6:127650225..127654504,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF146-2	chr6:127651907-127653253	predAs_engstrom06_BI770775_1

Variant related genes	Relation type
ECHDC1	TF binding region
ENSG00000093144	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1073931	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1073932	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10872312	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13218061	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1543432	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1964130	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2038378	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2057223	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2144742	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2144743	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2180341	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2281491	0.84[EUR][1000 genomes]
rs2326567	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3756996	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3798850	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3798852	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3798857	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4448121	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4472373	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4486042	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4895821	0.82[EUR][1000 genomes]
rs4895822	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4895823	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4897207	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6569477	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6569478	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6569479	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6569480	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6569482	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6569483	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569486	0.84[EUR][1000 genomes]
rs6900074	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6903878	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6904520	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6904630	0.83[EUR][1000 genomes]
rs6906717	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6910763	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6913424	0.84[EUR][1000 genomes]
rs6916990	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6930849	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6937287	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7449576	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7745944	0.84[EUR][1000 genomes]
rs7751865	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7752238	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7753913	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7756336	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7756880	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7756884	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7760748	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7766942	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7771923	0.84[EUR][1000 genomes]
rs7773484	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7774468	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7775493	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7776136	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs877661	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs910720	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9285459	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9285460	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9321073	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9321074	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9321076	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9321079	0.83[EUR][1000 genomes]
rs9375499	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9375503	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9385419	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9388561	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9388568	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9388571	0.81[AMR][1000 genomes]
rs9398836	0.82[EUR][1000 genomes]
rs9398837	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9398838	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9398839	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9398840	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9398841	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9398842	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9401950	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9401951	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9401952	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9401953	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9375501	ECHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:127605000-127660800	Weak transcription	Hela-S3	cervix
2	chr6:127608800-127652800	Weak transcription	Esophagus	oesophagus
3	chr6:127608800-127653600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:127608800-127653600	Weak transcription	Pancreas	Pancrea
5	chr6:127608800-127654600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:127608800-127661400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:127608800-127663600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:127608800-127663600	Weak transcription	Gastric	stomach
9	chr6:127613000-127661000	Weak transcription	Small Intestine	intestine
10	chr6:127614600-127659200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:127621800-127661000	Weak transcription	Fetal Heart	heart
12	chr6:127622000-127661400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr6:127622000-127661400	Weak transcription	NHEK	skin
14	chr6:127622800-127661400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:127622800-127662600	Weak transcription	Fetal Brain Male	brain
16	chr6:127625600-127661400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:127627400-127659000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:127628000-127653000	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:127629800-127661200	Weak transcription	A549	lung
20	chr6:127632400-127657600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:127634800-127661400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:127635000-127658000	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:127635400-127653600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:127635800-127659200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:127641000-127654000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:127643400-127654200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr6:127645400-127661400	Weak transcription	Right Ventricle	heart
28	chr6:127645800-127661000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:127646600-127660200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:127647400-127653800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr6:127647600-127653400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:127647600-127653600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:127647600-127654000	Weak transcription	Lung	lung
34	chr6:127647600-127654800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:127647600-127660200	Weak transcription	HSMMtube	muscle
36	chr6:127647600-127661000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:127647600-127661400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:127647600-127661400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr6:127647600-127661600	Weak transcription	Brain Germinal Matrix	brain
40	chr6:127647600-127661600	Weak transcription	Fetal Intestine Small	intestine
41	chr6:127647600-127662600	Weak transcription	Brain Angular Gyrus	brain
42	chr6:127647600-127662800	Weak transcription	Fetal Stomach	stomach
43	chr6:127647600-127662800	Weak transcription	Thymus	Thymus
44	chr6:127647600-127663000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr6:127647800-127658800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:127647800-127660600	Weak transcription	Psoas Muscle	Psoas
47	chr6:127647800-127661000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr6:127647800-127661400	Weak transcription	Left Ventricle	heart
49	chr6:127647800-127661400	Weak transcription	Ovary	ovary
50	chr6:127648000-127663200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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