Variant report

Variant	rs11154398
Chromosome Location	chr6:127654281-127654282
allele	A/C
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

No.	Distal block	Cell Line	Cell type
1	chr6:127652338..127654824-chr6:127662832..127665222,5	MCF-7	breast:
2	chr6:127646597..127649451-chr6:127650225..127654504,3	MCF-7	breast:
3	chr6:127653275..127659045-chr6:127660567..127666525,9	MCF-7	breast:

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

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11154395	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11154396	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11154397	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11556354	0.80[AMR][1000 genomes]
rs11961994	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199451	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12210968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12212752	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12215298	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12529077	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13192350	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13215850	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2057224	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2875981	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3756993	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798859	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4502958	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4577822	0.80[AFR][1000 genomes]
rs6683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6933893	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7775667	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11154398	ECHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 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	chr6:127608800-127654600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:127608800-127661400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:127608800-127663600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:127608800-127663600	Weak transcription	Gastric	stomach
6	chr6:127613000-127661000	Weak transcription	Small Intestine	intestine
7	chr6:127614600-127659200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:127621800-127661000	Weak transcription	Fetal Heart	heart
9	chr6:127622000-127661400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:127622000-127661400	Weak transcription	NHEK	skin
11	chr6:127622800-127661400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:127622800-127662600	Weak transcription	Fetal Brain Male	brain
13	chr6:127625600-127661400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:127627400-127659000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:127629800-127661200	Weak transcription	A549	lung
16	chr6:127632400-127657600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:127634800-127661400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:127635000-127658000	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:127635800-127659200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:127645400-127661400	Weak transcription	Right Ventricle	heart
21	chr6:127645800-127661000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr6:127646600-127660200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr6:127647600-127654800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:127647600-127660200	Weak transcription	HSMMtube	muscle
25	chr6:127647600-127661000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:127647600-127661400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:127647600-127661400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:127647600-127661600	Weak transcription	Brain Germinal Matrix	brain
29	chr6:127647600-127661600	Weak transcription	Fetal Intestine Small	intestine
30	chr6:127647600-127662600	Weak transcription	Brain Angular Gyrus	brain
31	chr6:127647600-127662800	Weak transcription	Fetal Stomach	stomach
32	chr6:127647600-127662800	Weak transcription	Thymus	Thymus
33	chr6:127647600-127663000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:127647800-127658800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:127647800-127660600	Weak transcription	Psoas Muscle	Psoas
36	chr6:127647800-127661000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr6:127647800-127661400	Weak transcription	Left Ventricle	heart
38	chr6:127647800-127661400	Weak transcription	Ovary	ovary
39	chr6:127648000-127663200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:127648200-127654800	Weak transcription	GM12878-XiMat	blood
41	chr6:127648200-127659600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:127648200-127659800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr6:127648200-127660000	Weak transcription	Fetal Brain Female	brain
44	chr6:127648200-127662000	Weak transcription	Brain Anterior Caudate	brain
45	chr6:127648400-127657800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:127648400-127658000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr6:127648400-127660400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:127648400-127660600	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:127648400-127660600	Weak transcription	Placenta	Placenta
50	chr6:127648400-127662600	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links