Variant report

Variant	rs10912854
Chromosome Location	chr1:174898715-174898716
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1012182	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10798324	0.85[CEU][hapmap]
rs10798327	0.85[CEU][hapmap]
rs10912843	0.85[CEU][hapmap]
rs10912853	0.90[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10912855	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10912857	0.80[AFR][1000 genomes]
rs12063093	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12078839	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12094876	0.90[CEU][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1231829	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1613634	0.85[CEU][hapmap]
rs1618408	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs1622802	0.85[CEU][hapmap]
rs162815	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs1653630	0.85[CEU][hapmap]
rs1653636	0.81[EUR][1000 genomes]
rs16847624	0.90[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs17302033	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs1754352	0.85[CEU][hapmap]
rs1754354	0.85[CEU][hapmap]
rs1754360	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1793292	0.85[CEU][hapmap]
rs1793294	0.86[CEU][hapmap]
rs1793298	0.85[CEU][hapmap]
rs1793305	0.85[CEU][hapmap]
rs1793307	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1793310	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1793313	0.87[EUR][1000 genomes]
rs1793315	0.80[EUR][1000 genomes]
rs1793316	0.85[CEU][hapmap]
rs1793320	0.85[CEU][hapmap]
rs1813136	0.86[CEU][hapmap]
rs1894198	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1894199	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1894201	0.84[CEU][hapmap]
rs1894680	0.85[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1923818	0.86[CEU][hapmap]
rs2003378	0.82[CEU][hapmap]
rs2156854	0.82[CHB][hapmap]
rs2157541	0.86[CEU][hapmap];0.96[YRI][hapmap]
rs2760057	0.85[CEU][hapmap]
rs2860725	0.85[CEU][hapmap]
rs2981892	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2987872	0.85[CEU][hapmap]
rs2987873	0.85[CEU][hapmap]
rs3117838	0.86[CEU][hapmap]
rs3118986	0.85[CEU][hapmap]
rs3118987	0.86[CEU][hapmap]
rs3118988	0.90[CEU][hapmap]
rs3118990	0.85[CEU][hapmap]
rs332763	0.83[EUR][1000 genomes]
rs332764	0.83[EUR][1000 genomes]
rs332772	0.83[EUR][1000 genomes]
rs332784	0.83[EUR][1000 genomes]
rs332798	0.82[EUR][1000 genomes]
rs332801	0.90[CEU][hapmap]
rs333436	0.85[CEU][hapmap]
rs333437	0.82[EUR][1000 genomes]
rs333471	0.83[EUR][1000 genomes]
rs459078	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs464635	0.85[CEU][hapmap]
rs4651205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4651231	0.90[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4651235	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4652797	0.85[CEU][hapmap]
rs55793234	0.81[EUR][1000 genomes]
rs58030712	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs60482554	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6425298	0.85[CEU][hapmap]
rs6425300	0.81[AMR][1000 genomes]
rs6425301	0.81[AMR][1000 genomes]
rs6425302	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs6425303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6425304	0.87[AMR][1000 genomes]
rs6425306	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6670315	0.85[CEU][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes]
rs6671196	0.81[EUR][1000 genomes]
rs6671272	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6671782	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6675528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66836419	0.82[EUR][1000 genomes]
rs6684229	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6684515	0.95[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6686872	0.81[AMR][1000 genomes]
rs6687616	0.86[CEU][hapmap]
rs6693979	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs6696465	0.85[CEU][hapmap]
rs6697561	0.85[CEU][hapmap]
rs6700953	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67054007	0.88[AFR][1000 genomes]
rs67133776	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67203477	0.82[EUR][1000 genomes]
rs67903803	0.82[EUR][1000 genomes]
rs72717637	0.91[EUR][1000 genomes]
rs72717649	0.82[EUR][1000 genomes]
rs72717650	0.82[EUR][1000 genomes]
rs72717653	0.82[EUR][1000 genomes]
rs72717661	0.81[EUR][1000 genomes]
rs7514183	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7516410	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs7543147	0.90[CEU][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7547658	0.85[CEU][hapmap]
rs913686	0.85[CEU][hapmap]
rs913687	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[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	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10912854	CACYBP	cis	brain	seeQTL
rs10912854	MRPS14	cis	brain	seeQTL
rs10912854	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs10912854	MRPS14	trans	brain	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174861400-174902400	Weak transcription	Left Ventricle	heart
2	chr1:174872800-174900400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:174874000-174910000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:174876800-174933600	Weak transcription	Aorta	Aorta
6	chr1:174883600-174900600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:174886000-174907200	Weak transcription	Primary T cells from cord blood	blood
8	chr1:174886400-174911600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:174889600-174907400	Weak transcription	Primary B cells from cord blood	blood
10	chr1:174889800-174900000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:174890000-174899600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:174890000-174900600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:174891800-174908600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:174892200-174905000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:174892600-174899400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:174892600-174900000	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:174893400-174900000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:174893400-174907600	Weak transcription	GM12878-XiMat	blood
19	chr1:174897000-174898800	Enhancers	Brain Anterior Caudate	brain
20	chr1:174897000-174898800	Enhancers	Brain Hippocampus Middle	brain
21	chr1:174897200-174900600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:174897400-174900000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:174897400-174900000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:174897400-174903600	Weak transcription	Pancreas	Pancrea
25	chr1:174897400-174910000	Weak transcription	Gastric	stomach
26	chr1:174897800-174898800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:174897800-174900200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:174897800-174900200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:174897800-174900400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:174897800-174900600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:174897800-174907200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:174898000-174900000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:174898000-174900200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:174898000-174900600	Weak transcription	Fetal Intestine Large	intestine
35	chr1:174898200-174898800	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr1:174898200-174900200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:174898200-174900400	Weak transcription	Brain Angular Gyrus	brain
38	chr1:174898400-174898800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:174898600-174899800	Strong transcription	Fetal Intestine Small	intestine
40	chr1:174898600-174900400	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links