Variant report

Variant	rs2280675
Chromosome Location	chr6:36891644-36891645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:36890243..36895519-chr6:36897368..36902270,7	K562	blood:
2	chr6:36889896..36892689-chr6:36954303..36956712,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10456446	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1046578	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10498736	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10947638	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947639	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10947640	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947645	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10947647	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947649	0.83[ASN][1000 genomes]
rs11757380	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11759850	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11963298	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11970506	0.91[EUR][1000 genomes]
rs12110889	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12193721	0.83[EUR][1000 genomes]
rs12194154	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12202755	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12213912	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13199306	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16889252	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2272275	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272276	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293392	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2395663	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3074	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34453243	0.81[ASN][1000 genomes]
rs3734331	0.98[ASN][1000 genomes]
rs3734333	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3957238	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4475317	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711473	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711474	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4714023	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59892114	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60992755	0.90[ASN][1000 genomes]
rs6457964	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67854134	0.94[ASN][1000 genomes]
rs6901884	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6904504	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6920322	0.91[ASN][1000 genomes]
rs6932038	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6932175	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7741378	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7743646	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7743836	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757241	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7761425	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7761653	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7770155	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7774420	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296200	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9462238	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9462239	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9462240	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9462241	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9470434	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9470439	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9918461	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9969040	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2280675	C6orf89	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36854400-36893000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:36866200-36896400	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:36867000-36897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:36877800-36896000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:36879400-36894000	Strong transcription	Fetal Brain Female	brain
6	chr6:36879600-36894000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:36879600-36895400	Strong transcription	Brain Germinal Matrix	brain
8	chr6:36880000-36892000	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr6:36880200-36893800	Strong transcription	K562	blood
10	chr6:36880600-36893600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr6:36880600-36900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:36881000-36892000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:36881000-36894800	Weak transcription	Fetal Brain Male	brain
14	chr6:36881400-36893000	Strong transcription	Spleen	Spleen
15	chr6:36881400-36893600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:36881400-36893800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:36881400-36896200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:36882000-36893800	Strong transcription	Liver	Liver
19	chr6:36882200-36892000	Strong transcription	Brain Anterior Caudate	brain
20	chr6:36882200-36894000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:36882400-36891800	Strong transcription	Primary T cells from cord blood	blood
22	chr6:36882400-36893000	Strong transcription	Fetal Intestine Large	intestine
23	chr6:36882400-36893600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:36882400-36893800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr6:36882400-36894800	Strong transcription	Fetal Intestine Small	intestine
26	chr6:36882400-36895600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:36882400-36896800	Weak transcription	Hela-S3	cervix
28	chr6:36882600-36893800	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:36882600-36893800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:36882600-36893800	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:36882600-36894000	Strong transcription	Dnd41	blood
32	chr6:36882800-36892800	Weak transcription	Fetal Kidney	kidney
33	chr6:36882800-36893800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:36883000-36893600	Weak transcription	A549	lung
35	chr6:36883200-36893400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:36883600-36893800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:36883800-36892800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:36883800-36892800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:36884000-36895400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr6:36884400-36894200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:36884800-36901200	Weak transcription	HMEC	breast
42	chr6:36886800-36892800	Strong transcription	Aorta	Aorta
43	chr6:36886800-36893800	Strong transcription	Fetal Stomach	stomach
44	chr6:36886800-36895400	Weak transcription	Psoas Muscle	Psoas
45	chr6:36887200-36892000	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr6:36887400-36894600	Weak transcription	Ovary	ovary
47	chr6:36887600-36895600	Weak transcription	Right Atrium	heart
48	chr6:36887800-36893800	Strong transcription	Lung	lung
49	chr6:36888000-36894200	Strong transcription	Left Ventricle	heart
50	chr6:36888000-36895400	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links