Variant report

Variant	rs877102
Chromosome Location	chr6:127587086-127587087
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	CEBPB	chr6:127587038-127588133	Hela-S3	cervix:	n/a	chr6:127587215-127587232
2	CTCF	chr6:127586861-127588113	K562	blood:	n/a	chr6:127587703-127587711 chr6:127587696-127587714 chr6:127587698-127587711 chr6:127587691-127587712 chr6:127587697-127587713
3	GATA1	chr6:127587024-127589818	PBDE	blood:	n/a	chr6:127589520-127589529
4	TBL1XR1	chr6:127587040-127588161	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:127586417..127590637-chr6:127662350..127666578,4	K562	blood:
2	chr6:127586572..127589762-chr6:127662304..127666058,6	K562	blood:

Variant related genes	Relation type
RNF146	TF binding region
ENSG00000093144	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1073931	0.82[EUR][1000 genomes]
rs1073932	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11961994	0.93[GIH][hapmap];0.92[TSI][hapmap]
rs12175928	0.82[JPT][hapmap]
rs12199451	0.93[GIH][hapmap];0.92[TSI][hapmap]
rs13218061	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs1543432	0.80[EUR][1000 genomes]
rs1964130	0.82[EUR][1000 genomes]
rs2038378	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2057223	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2073298	0.82[JPT][hapmap]
rs2144742	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2144743	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2180341	0.81[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2326567	0.81[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2875972	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3798850	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3798852	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3798853	0.81[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs3798857	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs3798859	0.93[GIH][hapmap];0.92[TSI][hapmap]
rs4141423	0.82[JPT][hapmap]
rs4280986	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4371861	0.80[ASN][1000 genomes]
rs4448121	0.80[EUR][1000 genomes]
rs4472373	0.80[EUR][1000 genomes]
rs4486042	0.80[EUR][1000 genomes]
rs4502958	0.81[EUR][1000 genomes]
rs4895821	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4895822	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4895823	0.83[EUR][1000 genomes]
rs4897207	0.90[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6569477	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6569478	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6569479	0.81[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6569480	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6569482	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6569483	0.85[EUR][1000 genomes]
rs6569485	0.82[JPT][hapmap]
rs6569486	0.80[EUR][1000 genomes]
rs67371475	0.83[EUR][1000 genomes]
rs6900074	0.82[EUR][1000 genomes]
rs6903878	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6904520	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6904834	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6906717	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6909703	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6910763	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6913350	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6913424	0.80[EUR][1000 genomes]
rs6916990	0.80[EUR][1000 genomes]
rs6930849	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6937287	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs7449576	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7453272	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs761842	0.82[JPT][hapmap]
rs7739679	0.80[EUR][1000 genomes]
rs7742161	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7745944	0.80[EUR][1000 genomes]
rs7751865	0.81[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs7752238	0.83[EUR][1000 genomes]
rs7753913	0.83[EUR][1000 genomes]
rs7756336	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs7756880	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7756884	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7760652	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7760748	0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs7764180	0.82[JPT][hapmap]
rs7766942	0.82[EUR][1000 genomes]
rs7770143	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7773484	0.83[EUR][1000 genomes]
rs7774468	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7775493	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7776136	0.81[CEU][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs877661	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs910720	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9285459	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9285460	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9321072	0.82[JPT][hapmap]
rs9321073	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9321074	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9321076	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs9372860	0.80[EUR][1000 genomes]
rs9372862	0.82[JPT][hapmap]
rs9372863	0.81[JPT][hapmap]
rs9372865	0.82[JPT][hapmap]
rs9375492	0.90[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs9375495	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9375499	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9375500	0.85[JPT][hapmap]
rs9375502	0.82[JPT][hapmap]
rs9375503	0.82[EUR][1000 genomes]
rs9385419	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9388553	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9388554	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9388555	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9388558	0.82[JPT][hapmap]
rs9388559	0.82[JPT][hapmap]
rs9388561	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9388568	0.80[CEU][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs9398836	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9398837	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9398838	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9398839	0.83[EUR][1000 genomes]
rs9398840	0.81[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs9398841	0.81[EUR][1000 genomes]
rs9398842	0.81[CEU][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs9401945	0.82[JPT][hapmap]
rs9401949	0.82[JPT][hapmap]
rs9401950	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs9401951	0.83[EUR][1000 genomes]
rs9401952	0.82[EUR][1000 genomes]
rs9401953	0.81[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs877102	ECHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:127571000-127587400	Weak transcription	Psoas Muscle	Psoas
2	chr6:127586000-127587200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:127586400-127587200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:127586400-127587400	Flanking Active TSS	Fetal Lung	lung
5	chr6:127586400-127590200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:127586600-127587200	Enhancers	Primary T cells from cord blood	blood
7	chr6:127586800-127587200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:127586800-127587200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:127586800-127587200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:127586800-127587200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:127586800-127587200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr6:127586800-127587200	Enhancers	Liver	Liver
13	chr6:127586800-127587200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr6:127586800-127587200	Enhancers	Osteobl	bone
15	chr6:127586800-127587400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr6:127586800-127587400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr6:127586800-127587400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:127586800-127587400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr6:127586800-127589800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:127586800-127590000	Active TSS	K562	blood
21	chr6:127586800-127590200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:127587000-127587200	Enhancers	Primary B cells from cord blood	blood
23	chr6:127587000-127587200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:127587000-127587200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr6:127587000-127587200	Enhancers	Fetal Brain Female	brain
26	chr6:127587000-127587200	Enhancers	Fetal Intestine Large	intestine
27	chr6:127587000-127587200	Enhancers	Fetal Stomach	stomach
28	chr6:127587000-127587200	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr6:127587000-127587200	Flanking Active TSS	A549	lung
30	chr6:127587000-127587200	Flanking Active TSS	Hela-S3	cervix
31	chr6:127587000-127587200	Enhancers	HUVEC	blood vessel
32	chr6:127587000-127587200	Enhancers	NHEK	skin
33	chr6:127587000-127587400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr6:127587000-127587400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr6:127587000-127587400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr6:127587000-127587400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:127587000-127587400	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr6:127587000-127587400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr6:127587000-127587400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:127587000-127587400	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr6:127587000-127587400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr6:127587000-127587400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:127587000-127587400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr6:127587000-127587400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr6:127587000-127587400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr6:127587000-127587400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr6:127587000-127587400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:127587000-127587400	Enhancers	Brain Angular Gyrus	brain
49	chr6:127587000-127587400	Enhancers	Brain Substantia Nigra	brain
50	chr6:127587000-127587400	Flanking Active TSS	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links