Variant report

Variant	rs68042406
Chromosome Location	chr6:109803595-109803596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109775795..109777582-chr6:109802976..109804493,2	MCF-7	breast:
2	chr6:109702597..109705942-chr6:109803330..109806291,3	K562	blood:
3	chr6:109759652..109764361-chr6:109800705..109806354,8	K562	blood:
4	chr6:109703226..109705290-chr6:109802868..109805423,2	K562	blood:
5	chr6:109787055..109789260-chr6:109802525..109804653,2	K562	blood:
6	chr6:109774016..109776250-chr6:109801827..109803875,2	K562	blood:
7	chr6:109759628..109764398-chr6:109803414..109806709,4	K562	blood:
8	chr6:109802318..109804692-chr6:109827428..109829307,3	MCF-7	breast:
9	chr6:109774750..109777186-chr6:109800628..109803875,3	K562	blood:
10	chr6:109760182..109762059-chr6:109802883..109805670,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135535	Chromatin interaction
ENSG00000135596	Chromatin interaction
ENSG00000135587	Chromatin interaction
ENSG00000185250	Chromatin interaction
ENSG00000155085	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10080429	0.83[EUR][1000 genomes]
rs1040284	0.83[EUR][1000 genomes]
rs10457190	0.82[EUR][1000 genomes]
rs10457192	0.95[ASN][1000 genomes]
rs10457194	0.92[ASN][1000 genomes]
rs10457195	0.90[ASN][1000 genomes]
rs1048203	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10499053	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10782161	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10782162	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782163	0.94[ASN][1000 genomes]
rs10872034	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153174	0.83[EUR][1000 genomes]
rs11153175	0.83[EUR][1000 genomes]
rs11153176	0.83[EUR][1000 genomes]
rs11153177	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11153180	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11153181	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11153183	0.95[ASN][1000 genomes]
rs11153188	0.89[ASN][1000 genomes]
rs11752791	0.88[ASN][1000 genomes]
rs11754340	0.85[ASN][1000 genomes]
rs11754455	0.95[ASN][1000 genomes]
rs11755641	0.86[ASN][1000 genomes]
rs11967108	0.83[EUR][1000 genomes]
rs12190920	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12190996	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12191353	0.81[ASN][1000 genomes]
rs12192776	0.82[ASN][1000 genomes]
rs12192847	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12193493	0.83[EUR][1000 genomes]
rs12193719	0.86[ASN][1000 genomes]
rs12194061	0.89[ASN][1000 genomes]
rs12194157	0.82[ASN][1000 genomes]
rs12197114	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12197180	0.93[ASN][1000 genomes]
rs12197950	0.82[ASN][1000 genomes]
rs12198938	0.95[ASN][1000 genomes]
rs12199154	0.95[ASN][1000 genomes]
rs12205485	0.85[ASN][1000 genomes]
rs12206928	0.81[EUR][1000 genomes]
rs12208018	0.85[ASN][1000 genomes]
rs12208933	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12209691	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12212476	0.95[ASN][1000 genomes]
rs12213313	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12214639	0.86[ASN][1000 genomes]
rs12524273	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12524639	0.84[EUR][1000 genomes]
rs12528781	0.85[ASN][1000 genomes]
rs12528822	0.82[EUR][1000 genomes]
rs13191066	0.85[ASN][1000 genomes]
rs13199135	0.86[ASN][1000 genomes]
rs13201947	0.88[ASN][1000 genomes]
rs13201951	0.91[ASN][1000 genomes]
rs13203587	0.95[ASN][1000 genomes]
rs13204102	0.86[ASN][1000 genomes]
rs13204500	0.86[ASN][1000 genomes]
rs13212766	0.84[EUR][1000 genomes]
rs1321328	0.82[ASN][1000 genomes]
rs13220915	0.95[ASN][1000 genomes]
rs1322816	0.85[EUR][1000 genomes]
rs1358997	0.84[EUR][1000 genomes]
rs1358998	0.84[EUR][1000 genomes]
rs1406899	0.95[ASN][1000 genomes]
rs1476388	0.94[ASN][1000 genomes]
rs1546980	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1590306	0.83[EUR][1000 genomes]
rs17070580	0.83[EUR][1000 genomes]
rs1923725	0.85[EUR][1000 genomes]
rs1960325	0.86[ASN][1000 genomes]
rs1980591	0.85[ASN][1000 genomes]
rs1998811	0.95[ASN][1000 genomes]
rs2024849	0.95[ASN][1000 genomes]
rs2024850	0.95[ASN][1000 genomes]
rs2024852	0.95[ASN][1000 genomes]
rs2024853	0.95[ASN][1000 genomes]
rs2148089	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2208209	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2236582	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2275650	0.83[EUR][1000 genomes]
rs2277114	0.95[ASN][1000 genomes]
rs2357124	0.88[ASN][1000 genomes]
rs34202013	0.83[EUR][1000 genomes]
rs35056702	0.83[EUR][1000 genomes]
rs36035949	0.85[EUR][1000 genomes]
rs36099706	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3757234	0.85[EUR][1000 genomes]
rs3778475	0.83[EUR][1000 genomes]
rs3778477	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3799839	0.84[EUR][1000 genomes]
rs3807005	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3818934	0.83[EUR][1000 genomes]
rs4490694	0.86[ASN][1000 genomes]
rs4945833	0.86[ASN][1000 genomes]
rs59056467	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59906308	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6906216	0.93[ASN][1000 genomes]
rs6911838	0.89[EUR][1000 genomes]
rs6914498	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6916579	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6920292	0.84[ASN][1000 genomes]
rs6926096	0.93[ASN][1000 genomes]
rs6929023	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs729888	0.82[ASN][1000 genomes]
rs7372	0.83[EUR][1000 genomes]
rs749517	0.94[ASN][1000 genomes]
rs752262	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7755941	0.95[ASN][1000 genomes]
rs7773095	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7773950	0.95[ASN][1000 genomes]
rs9320287	0.83[EUR][1000 genomes]
rs9480948	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9480951	0.83[EUR][1000 genomes]
rs9480953	0.83[EUR][1000 genomes]
rs9480955	0.83[EUR][1000 genomes]
rs9480957	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9487068	0.81[EUR][1000 genomes]
rs9487094	0.83[EUR][1000 genomes]
rs9487095	0.83[EUR][1000 genomes]
rs9487100	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs971434	0.82[ASN][1000 genomes]
rs9885646	0.83[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	esv3377564	chr6:109803284-109806132	Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs68042406	SMPD2	cis	Whole Blood	GTEx
rs68042406	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs68042406	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109799600-109803800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:109801200-109803600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:109801200-109803600	Enhancers	Fetal Heart	heart
4	chr6:109801400-109804400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
5	chr6:109801600-109804200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:109801800-109803800	Enhancers	Stomach Mucosa	stomach
7	chr6:109802200-109803600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
8	chr6:109802400-109803600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:109802400-109803600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr6:109802600-109803800	Enhancers	Spleen	Spleen
11	chr6:109802800-109803600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:109802800-109804000	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr6:109803000-109803600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr6:109803000-109803600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr6:109803000-109803600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:109803000-109803600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr6:109803000-109803600	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr6:109803000-109803800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr6:109803000-109804000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr6:109803000-109804200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr6:109803000-109805000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:109803200-109803600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:109803200-109803600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:109803200-109803600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:109803200-109803600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:109803200-109803600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:109803200-109803600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:109803200-109803600	Enhancers	Liver	Liver
29	chr6:109803200-109803600	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr6:109803200-109803600	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr6:109803200-109803600	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr6:109803200-109803600	Flanking Active TSS	Fetal Brain Female	brain
33	chr6:109803200-109803600	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr6:109803200-109803600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
35	chr6:109803200-109803600	Enhancers	Fetal Lung	lung
36	chr6:109803200-109803600	Flanking Active TSS	Placenta	Placenta
37	chr6:109803200-109803600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr6:109803200-109803600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr6:109803200-109803800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr6:109803200-109803800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:109803200-109803800	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr6:109803200-109803800	Weak transcription	Gastric	stomach
43	chr6:109803200-109803800	Flanking Active TSS	Left Ventricle	heart
44	chr6:109803200-109803800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr6:109803200-109803800	Flanking Active TSS	HMEC	breast
46	chr6:109803200-109804000	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr6:109803200-109804000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr6:109803200-109804000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr6:109803200-109804000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr6:109803200-109804200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links