Variant report

Variant	rs10457190
Chromosome Location	chr6:109665129-109665130
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109662626..109665384-chr6:109701229..109703998,3	MCF-7	breast:
2	chr6:109656306..109660874-chr6:109662231..109666521,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203799	Chromatin interaction
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10080429	0.90[EUR][1000 genomes]
rs1040284	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1048203	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10782161	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10782162	0.82[EUR][1000 genomes]
rs10872032	0.94[EUR][1000 genomes]
rs10872034	0.82[EUR][1000 genomes]
rs11153171	0.88[EUR][1000 genomes]
rs11153174	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153175	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153176	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153177	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11153180	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11153181	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11967108	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12190920	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12190996	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12192847	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12193493	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12197114	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12206928	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12209691	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12213313	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12524273	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12524639	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12528822	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13212766	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1322816	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1358997	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1358998	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1546980	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1590306	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17070580	0.91[EUR][1000 genomes]
rs1923725	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2236582	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275650	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34202013	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35056702	0.91[EUR][1000 genomes]
rs36035949	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36099706	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757234	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778475	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778477	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3799839	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3807005	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3818934	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59056467	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59906308	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68042406	0.82[EUR][1000 genomes]
rs6920962	0.83[EUR][1000 genomes]
rs6929023	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7372	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs752262	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7773095	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9320287	0.91[EUR][1000 genomes]
rs9480933	0.95[EUR][1000 genomes]
rs9480948	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9480951	0.91[EUR][1000 genomes]
rs9480953	0.91[EUR][1000 genomes]
rs9480955	0.91[EUR][1000 genomes]
rs9480957	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9487068	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9487094	0.91[EUR][1000 genomes]
rs9487095	0.91[EUR][1000 genomes]
rs9487097	0.86[EUR][1000 genomes]
rs9487098	0.87[EUR][1000 genomes]
rs9487100	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9885646	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv5435	chr6:109633035-109669127	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10457190	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs10457190	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs10457190	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs10457190	SMPD2	cis	Whole Blood	GTEx
rs10457190	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109644600-109675200	Weak transcription	Primary T cells from cord blood	blood
2	chr6:109654000-109669400	Weak transcription	Small Intestine	intestine
3	chr6:109654200-109671000	Weak transcription	Spleen	Spleen
4	chr6:109654200-109675000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:109654200-109676200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:109654400-109668800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr6:109657800-109671000	Weak transcription	Lung	lung
8	chr6:109658400-109665200	Weak transcription	Fetal Intestine Small	intestine
9	chr6:109658400-109669200	Weak transcription	Liver	Liver
10	chr6:109658600-109668200	Weak transcription	Colonic Mucosa	Colon
11	chr6:109658600-109670600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:109658800-109670600	Weak transcription	Right Atrium	heart
13	chr6:109658800-109677000	Weak transcription	Fetal Stomach	stomach
14	chr6:109660200-109677200	Weak transcription	Thymus	Thymus
15	chr6:109660400-109674600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:109660600-109665800	Enhancers	Fetal Muscle Leg	muscle
17	chr6:109660600-109666000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:109660800-109666000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr6:109661200-109668600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:109661400-109671400	Weak transcription	Fetal Thymus	thymus
21	chr6:109662600-109682000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:109662800-109669600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:109662800-109670600	Weak transcription	Aorta	Aorta
24	chr6:109662800-109670600	Weak transcription	Right Ventricle	heart
25	chr6:109662800-109671000	Weak transcription	Psoas Muscle	Psoas
26	chr6:109662800-109677000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:109663000-109670600	Weak transcription	Adipose Nuclei	Adipose
28	chr6:109663400-109665200	Enhancers	K562	blood
29	chr6:109663400-109665600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:109663400-109665800	Enhancers	Fetal Muscle Trunk	muscle
31	chr6:109663600-109665600	Enhancers	Gastric	stomach
32	chr6:109663600-109666000	Enhancers	Stomach Mucosa	stomach
33	chr6:109663600-109666400	Enhancers	Placenta	Placenta
34	chr6:109663800-109665600	Enhancers	Placenta Amnion	Placenta Amnion
35	chr6:109664000-109669000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:109664000-109670800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:109664200-109669000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr6:109664200-109670800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr6:109664200-109672800	Weak transcription	HSMM	muscle
40	chr6:109664400-109668000	Weak transcription	Brain Substantia Nigra	brain
41	chr6:109664400-109668000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:109664400-109668600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:109664400-109670400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:109664400-109670600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:109664400-109671000	Weak transcription	Left Ventricle	heart
46	chr6:109665000-109665600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr6:109665000-109665600	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links