Variant report

Variant	rs12041534
Chromosome Location	chr1:155407096-155407097
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	chr1:155406981..155408656-chr1:155410586..155413532,3	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10752611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10796943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10796944	0.85[AMR][1000 genomes]
rs10796945	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796946	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796947	0.91[ASN][1000 genomes]
rs10908463	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap]
rs10908465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908466	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908467	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10908469	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10908470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10908472	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264359	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs11264361	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs11264363	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs11264366	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11264367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11264369	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11264370	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11264371	0.93[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264372	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264374	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264380	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264383	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264386	0.81[ASN][1000 genomes]
rs11264387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]
rs11582072	0.91[ASN][1000 genomes]
rs12025532	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12026638	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028416	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12030596	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12037824	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12046473	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12067371	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12079134	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12081067	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12143948	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12239100	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12239114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs12724079	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12746592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1325908	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1360554	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs1556488	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs1886905	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs2025669	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2297480	0.88[CEU][hapmap];0.89[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs35615695	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs3851912	0.80[AMR][1000 genomes]
rs3892792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs5005770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56675301	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6670014	0.85[AMR][1000 genomes]
rs6677385	0.86[AFR][1000 genomes]
rs6684889	0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs6688636	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs6692183	0.86[AFR][1000 genomes]
rs66923802	0.87[EUR][1000 genomes]
rs6696888	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs71517782	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7411786	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7416976	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7556102	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
4	esv1799856	chr1:155305059-155534616	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv1795662	chr1:155305059-155540660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	esv1795478	chr1:155334933-155510824	Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1803551	chr1:155334933-155522572	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv1800974	chr1:155367680-155510824	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12041534	SPRR2A	cis	cerebellum	SCAN
rs12041534	GBA	cis	Esophagus Mucosa	GTEx
rs12041534	YY1AP1	cis	parietal	SCAN
rs12041534	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs12041534	SPRR2D	cis	parietal	SCAN
rs12041534	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs12041534	YY1AP1	cis	cerebellum	SCAN
rs12041534	GBAP1	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155312400-155407400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155347400-155407400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:155349400-155407600	Weak transcription	Aorta	Aorta
4	chr1:155359400-155407200	Weak transcription	Pancreas	Pancrea
5	chr1:155362200-155433400	Weak transcription	Psoas Muscle	Psoas
6	chr1:155362800-155442400	Weak transcription	Right Ventricle	heart
7	chr1:155363000-155407400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:155364400-155450800	Weak transcription	HUVEC	blood vessel
9	chr1:155365000-155407800	Weak transcription	Fetal Kidney	kidney
10	chr1:155365600-155407200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:155367400-155426000	Weak transcription	Stomach Mucosa	stomach
12	chr1:155381800-155407200	Weak transcription	HMEC	breast
13	chr1:155382600-155408000	Weak transcription	Ovary	ovary
14	chr1:155383400-155407600	Weak transcription	Gastric	stomach
15	chr1:155384800-155425600	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:155385800-155408000	Weak transcription	Brain Germinal Matrix	brain
17	chr1:155391000-155407600	Weak transcription	Fetal Brain Female	brain
18	chr1:155392800-155422800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:155394200-155407400	Weak transcription	HSMMtube	muscle
20	chr1:155394600-155407200	Weak transcription	Brain Anterior Caudate	brain
21	chr1:155397000-155408800	Strong transcription	Fetal Stomach	stomach
22	chr1:155397400-155409000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:155397400-155410400	Strong transcription	Fetal Intestine Small	intestine
24	chr1:155397600-155409200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:155399000-155409000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:155399000-155409400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr1:155399400-155407200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:155399400-155408200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:155399400-155418200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:155399600-155407200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:155399600-155409000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:155399800-155411000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:155400000-155410000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:155400200-155407200	Weak transcription	Brain Angular Gyrus	brain
35	chr1:155400600-155410000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:155401400-155407400	Weak transcription	Left Ventricle	heart
37	chr1:155402200-155409000	Strong transcription	Liver	Liver
38	chr1:155402400-155426800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:155402600-155409000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:155402800-155407400	Weak transcription	Right Atrium	heart
41	chr1:155402800-155407600	Weak transcription	Brain Substantia Nigra	brain
42	chr1:155403400-155407200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr1:155403400-155408000	Weak transcription	Small Intestine	intestine
44	chr1:155403400-155411800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:155403600-155407200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:155403600-155407600	Weak transcription	NHLF	lung
47	chr1:155403800-155407200	Weak transcription	Adipose Nuclei	Adipose
48	chr1:155403800-155407600	Weak transcription	Lung	lung
49	chr1:155403800-155410200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr1:155404000-155407400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links