Variant report

Variant	rs6684481
Chromosome Location	chr1:169808400-169808401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10737549	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10737550	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737551	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10800479	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10800480	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10800481	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10800483	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10800484	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10919245	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10919248	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10919251	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10919257	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919263	0.90[ASN][1000 genomes]
rs12047487	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12133843	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1883436	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2056981	0.89[ASN][1000 genomes]
rs2143122	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2179396	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2281039	0.88[ASN][1000 genomes]
rs2294322	0.93[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2294496	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2420512	0.95[ASN][1000 genomes]
rs2901179	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3766132	0.88[ASN][1000 genomes]
rs3766134	0.88[ASN][1000 genomes]
rs3766137	0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3766142	0.95[ASN][1000 genomes]
rs3766144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766148	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3766151	0.85[ASN][1000 genomes]
rs3766154	0.84[ASN][1000 genomes]
rs3766155	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4376791	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4508080	0.92[ASN][1000 genomes]
rs4614317	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4615900	0.95[ASN][1000 genomes]
rs4656196	0.89[ASN][1000 genomes]
rs4656197	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656199	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656200	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656721	0.90[ASN][1000 genomes]
rs4656724	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656725	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6427220	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427225	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6427226	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6427227	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427228	0.86[ASN][1000 genomes]
rs6656965	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6664099	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668114	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6669794	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6671752	0.87[ASN][1000 genomes]
rs6680650	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6680938	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682137	0.95[ASN][1000 genomes]
rs6682835	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6683056	0.90[ASN][1000 genomes]
rs6687377	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6702969	0.90[ASN][1000 genomes]
rs717481	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs732185	0.94[ASN][1000 genomes]
rs7519364	0.89[ASN][1000 genomes]
rs7521700	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7525259	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7530237	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7545011	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9287097	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv872542	chr1:169802760-169844093	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6684481	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:128 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169764800-169818200	Weak transcription	Esophagus	oesophagus
2	chr1:169764800-169818200	Weak transcription	Lung	lung
3	chr1:169764800-169823600	Weak transcription	Gastric	stomach
4	chr1:169765000-169821800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:169765200-169809000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:169765200-169814800	Weak transcription	Brain Anterior Caudate	brain
7	chr1:169765200-169815200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:169765200-169818800	Weak transcription	Brain Angular Gyrus	brain
9	chr1:169765200-169820600	Weak transcription	Psoas Muscle	Psoas
10	chr1:169765200-169823400	Weak transcription	Right Ventricle	heart
11	chr1:169765400-169822600	Weak transcription	Colonic Mucosa	Colon
12	chr1:169765600-169818200	Weak transcription	NHLF	lung
13	chr1:169765800-169815200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:169765800-169818400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:169777400-169815400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:169784000-169814000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:169784000-169814800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:169786600-169841400	Strong transcription	Dnd41	blood
20	chr1:169788600-169823600	Weak transcription	Pancreas	Pancrea
21	chr1:169789200-169818600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:169790800-169808800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:169791200-169808800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:169791200-169810800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:169791200-169841200	Strong transcription	Fetal Thymus	thymus
26	chr1:169793800-169814400	Weak transcription	Brain Substantia Nigra	brain
27	chr1:169793800-169822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:169794000-169814800	Weak transcription	Aorta	Aorta
29	chr1:169794200-169818400	Weak transcription	NHEK	skin
30	chr1:169794800-169822000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:169797000-169818200	Weak transcription	Spleen	Spleen
32	chr1:169797600-169818200	Weak transcription	HSMMtube	muscle
33	chr1:169797800-169813400	Weak transcription	Fetal Intestine Large	intestine
34	chr1:169798000-169809200	Weak transcription	Fetal Intestine Small	intestine
35	chr1:169799200-169814800	Weak transcription	Osteobl	bone
36	chr1:169799400-169814800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:169800000-169814800	Weak transcription	HMEC	breast
38	chr1:169800800-169811400	Weak transcription	HSMM	muscle
39	chr1:169802200-169812800	Weak transcription	NH-A	brain
40	chr1:169802200-169822600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:169802400-169821800	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:169802600-169813000	Weak transcription	Left Ventricle	heart
43	chr1:169802800-169815000	Weak transcription	Hela-S3	cervix
44	chr1:169802800-169819800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:169803000-169813000	Weak transcription	Ovary	ovary
46	chr1:169804000-169809400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:169804000-169811600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:169804200-169812800	Weak transcription	HepG2	liver
49	chr1:169805200-169809000	Strong transcription	Fetal Lung	lung
50	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links