Variant report

Variant	rs9865109
Chromosome Location	chr3:42613846-42613847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42609124..42614031-chr3:42620291..42625613,5	MCF-7	breast:
2	chr3:42611786..42615300-chr3:42621924..42624198,4	K562	blood:
3	chr3:42612219..42614700-chr3:42641488..42643709,2	MCF-7	breast:
4	chr3:42613535..42614413-chr3:42676322..42677312,2	K562	blood:
5	chr3:42612205..42615201-chr3:42631564..42633106,2	MCF-7	breast:
6	chr3:42613802..42614405-chr3:42796904..42797443,2	MCF-7	breast:
7	chr3:42613463..42614205-chr3:42785557..42786369,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000114857	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2136012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271181	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2271185	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271186	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2976533	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs339658	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs339725	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339726	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339727	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs339728	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339733	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342521	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs342522	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs342536	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs342537	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3774398	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4549	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs586082	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs587712	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs597498	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs607568	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs612733	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs614323	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs617722	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627664	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638836	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs639692	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs640689	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441892	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs663673	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689251	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs704979	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8351	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs925457	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9865109	NKTR	cis	Nerve Tibial	GTEx
rs9865109	SEC22C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42588600-42618000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:42589400-42614000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:42589800-42616400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:42591000-42614000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:42594600-42615200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:42598000-42615600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:42598200-42616400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:42602800-42616800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:42603000-42622800	Weak transcription	Colonic Mucosa	Colon
10	chr3:42603400-42616600	Weak transcription	Fetal Brain Male	brain
11	chr3:42604200-42622800	Weak transcription	Psoas Muscle	Psoas
12	chr3:42604200-42623000	Weak transcription	Esophagus	oesophagus
13	chr3:42604400-42615200	Weak transcription	Hela-S3	cervix
14	chr3:42604400-42616800	Weak transcription	Brain Angular Gyrus	brain
15	chr3:42604600-42622400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:42605000-42621400	Weak transcription	HMEC	breast
17	chr3:42605200-42622400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:42605600-42615400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:42607800-42615200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:42607800-42615200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:42607800-42621600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:42607800-42622800	Weak transcription	Pancreas	Pancrea
23	chr3:42608000-42623000	Weak transcription	Gastric	stomach
24	chr3:42608600-42621400	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:42608600-42622800	Weak transcription	Aorta	Aorta
26	chr3:42609000-42621600	Weak transcription	NHLF	lung
27	chr3:42609000-42622800	Weak transcription	HSMMtube	muscle
28	chr3:42609000-42623000	Weak transcription	Spleen	Spleen
29	chr3:42609200-42614400	Weak transcription	Fetal Intestine Large	intestine
30	chr3:42609200-42615400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:42609200-42616000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:42609200-42616200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:42609200-42616200	Weak transcription	Fetal Kidney	kidney
34	chr3:42609200-42616200	Weak transcription	Placenta	Placenta
35	chr3:42609200-42621200	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:42609200-42621600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:42609200-42621600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:42609200-42621800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:42609200-42622400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:42609400-42614400	Weak transcription	Fetal Lung	lung
41	chr3:42609400-42615200	Weak transcription	Primary B cells from cord blood	blood
42	chr3:42609400-42616400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:42609400-42616600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:42609600-42623000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:42610000-42622000	Weak transcription	Osteobl	bone
46	chr3:42610200-42614400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:42610400-42614200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:42610400-42622600	Weak transcription	Right Ventricle	heart
49	chr3:42610600-42614000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:42610600-42614000	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links