Variant report

Variant	rs12131978
Chromosome Location	chr1:47770263-47770264
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47768301..47773311-chr1:47776226..47780764,7	K562	blood:
2	chr1:47768273..47770405-chr1:47831380..47833111,2	K562	blood:

Variant related genes	Relation type
ENSG00000123473	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10157734	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10218615	0.86[ASN][1000 genomes]
rs10789509	0.86[ASN][1000 genomes]
rs11211489	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211490	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211492	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211495	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211500	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211505	0.95[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211512	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211526	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211537	0.86[ASN][1000 genomes]
rs11576796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11577236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11577960	0.95[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578360	0.95[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579854	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11580114	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580148	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583162	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584518	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11587014	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587107	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587272	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11588964	0.86[ASN][1000 genomes]
rs12117686	0.95[CEU][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12118205	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118206	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123269	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12123358	0.90[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129259	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12129594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132521	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12132909	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134888	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12135037	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12139700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12140580	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12143808	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144920	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12145103	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12145974	0.95[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184262	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184269	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184297	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406951	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12407463	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409300	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12410850	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718447	0.95[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12729251	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738065	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12749507	0.95[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12751618	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12756634	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757893	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13374382	0.95[CEU][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376679	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103095	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103168	0.94[CEU][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17370386	0.95[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2097	0.86[ASN][1000 genomes]
rs2098	0.86[ASN][1000 genomes]
rs2405787	0.95[CEU][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622903	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2622914	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2820986	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2897238	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33980430	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34192192	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34979288	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35234940	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35601384	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35856603	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4375315	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4481897	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4926840	0.85[EUR][1000 genomes]
rs56804458	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58891696	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60352530	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6660651	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665067	0.80[ASN][1000 genomes]
rs6670458	0.86[ASN][1000 genomes]
rs6688323	0.90[EUR][1000 genomes]
rs6688804	0.95[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698471	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6698717	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67221389	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67295054	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67905093	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71502303	0.86[ASN][1000 genomes]
rs72686209	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7354822	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415976	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7514213	0.86[ASN][1000 genomes]
rs7534328	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7548099	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9725517	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933511	chr1:47767039-47770608	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
2	nsv933023	chr1:47767174-47770608	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
3	nsv933103	chr1:47767544-47770756	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv933978	chr1:47770133-47770608	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
5	nsv934241	chr1:47770254-47770608	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12131978	MKNK1	cis	cerebellum	SCAN
rs12131978	TMEM125	cis	cerebellum	SCAN
rs12131978	STIL	Cis_1M	lymphoblastoid	RTeQTL
rs12131978	CMPK1	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47714400-47779200	Weak transcription	Small Intestine	intestine
2	chr1:47714600-47778400	Weak transcription	Fetal Heart	heart
3	chr1:47716600-47772600	Strong transcription	Dnd41	blood
4	chr1:47723400-47772400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:47731400-47778000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:47735400-47779000	Weak transcription	Esophagus	oesophagus
7	chr1:47741400-47771400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:47741600-47770800	Strong transcription	Fetal Thymus	thymus
9	chr1:47741800-47770800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:47742600-47773000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:47742600-47773000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:47743800-47779200	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:47744200-47779000	Weak transcription	Brain Angular Gyrus	brain
14	chr1:47744400-47779000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:47744800-47779000	Weak transcription	HSMMtube	muscle
16	chr1:47746200-47772000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:47746200-47778800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:47746600-47772200	Weak transcription	Ovary	ovary
19	chr1:47746600-47776400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:47746600-47778400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:47746600-47778400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:47746600-47778400	Weak transcription	Fetal Brain Female	brain
23	chr1:47746800-47778800	Weak transcription	Placenta	Placenta
24	chr1:47749600-47777800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:47750000-47779200	Weak transcription	Right Atrium	heart
26	chr1:47755200-47779000	Weak transcription	Primary B cells from cord blood	blood
27	chr1:47755400-47778800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:47757400-47773000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:47757800-47771400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:47758000-47771000	Strong transcription	K562	blood
31	chr1:47760000-47772600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:47760800-47770600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:47763400-47778600	Weak transcription	Adipose Nuclei	Adipose
34	chr1:47763600-47779000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:47763600-47779200	Weak transcription	Fetal Brain Male	brain
36	chr1:47764200-47770800	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:47764200-47779000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:47764200-47779000	Weak transcription	Stomach Mucosa	stomach
39	chr1:47764400-47772600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:47764600-47771000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:47765000-47772600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:47765200-47770600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:47765200-47770600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:47765200-47771200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:47765400-47770400	Strong transcription	Primary hematopoietic stem cells	blood
46	chr1:47765400-47770600	Strong transcription	HUVEC	blood vessel
47	chr1:47765400-47770800	Strong transcription	Osteobl	bone
48	chr1:47765400-47772600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:47765400-47773000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:47765400-47777400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links