Variant report

Variant	rs738027
Chromosome Location	chr12:21592357-21592358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:21569338..21572113-chr12:21589171..21592854,4	K562	blood:
2	chr12:21569338..21572113-chr12:21589171..21592483,4	K562	blood:
3	chr12:21591250..21594769-chr12:21604296..21607496,3	K562	blood:
4	chr12:21590977..21592503-chr12:21654111..21656929,2	K562	blood:

Variant related genes	Relation type
ENSG00000004700	Chromatin interaction
ENSG00000084453	Chromatin interaction
ENSG00000111711	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1024734	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11046040	0.84[ASN][1000 genomes]
rs11046044	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611002	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11835956	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12422251	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12423173	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12423381	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423536	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12424852	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12426100	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12426103	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12817513	0.83[ASN][1000 genomes]
rs12818516	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12826040	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1860948	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2110164	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2110165	0.81[MKK][hapmap]
rs2192183	0.80[MKK][hapmap]
rs2215734	0.80[MKK][hapmap]
rs2302500	0.80[MKK][hapmap]
rs2417981	0.80[MKK][hapmap]
rs2417987	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759229	0.80[MKK][hapmap]
rs3782660	0.80[MKK][hapmap]
rs4539382	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4762826	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6487222	0.80[MKK][hapmap]
rs6487223	0.80[MKK][hapmap]
rs6487224	0.91[CEU][hapmap];0.92[YRI][hapmap]
rs6487229	0.80[MKK][hapmap]
rs6487231	0.80[MKK][hapmap]
rs7131809	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133131	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133853	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136257	0.80[MKK][hapmap]
rs7138089	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7298136	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310391	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314131	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs738028	0.80[MKK][hapmap]
rs7957415	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7959893	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971245	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7973116	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974260	0.87[CEU][hapmap]
rs7974817	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9668302	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898895	chr12:21561645-21621891	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv469163	chr12:21579080-21592357	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
6	nsv557742	chr12:21579080-21592357	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs738027	PYROXD1	cis	lymphoblastoid	seeQTL
rs738027	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs738027	PYROXD1	cis	cerebellum	SCAN
rs738027	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs738027	OR8G5	trans	parietal	SCAN
rs738027	FLJ22028	cis	normal skin	skin_eQTL
rs738027	TPH1	trans	cerebellum	SCAN
rs738027	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs738027	PYROXD1	cis	parietal	SCAN
rs738027	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs738027	PYROXD1	cis	Esophagus Muscularis	GTEx
rs738027	IAPP	cis	uninvolved skin	skin_eQTL
rs738027	RECQL	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21590000-21592400	Active TSS	Stomach Smooth Muscle	stomach
2	chr12:21590000-21592800	Active TSS	GM12878-XiMat	blood
3	chr12:21591200-21592600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr12:21591200-21593000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr12:21591400-21592600	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr12:21591400-21592600	Flanking Active TSS	Dnd41	blood
7	chr12:21591400-21594800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:21591400-21594800	Weak transcription	Esophagus	oesophagus
9	chr12:21591400-21594800	Weak transcription	Gastric	stomach
10	chr12:21591400-21594800	Weak transcription	Left Ventricle	heart
11	chr12:21591400-21594800	Weak transcription	Lung	lung
12	chr12:21591400-21594800	Weak transcription	Spleen	Spleen
13	chr12:21591400-21595400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:21591400-21602800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:21591600-21592600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:21591600-21592600	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr12:21591600-21592600	Enhancers	Small Intestine	intestine
18	chr12:21591600-21592800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:21591600-21592800	Enhancers	Primary B cells from peripheral blood	blood
20	chr12:21591600-21592800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr12:21591600-21594000	Weak transcription	Fetal Intestine Large	intestine
22	chr12:21591600-21594200	Weak transcription	Fetal Stomach	stomach
23	chr12:21591600-21594400	Weak transcription	Placenta	Placenta
24	chr12:21591600-21594600	Weak transcription	Brain Anterior Caudate	brain
25	chr12:21591600-21594600	Weak transcription	Ovary	ovary
26	chr12:21591600-21594800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:21591600-21594800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:21591600-21594800	Weak transcription	Aorta	Aorta
29	chr12:21591600-21594800	Weak transcription	Brain Germinal Matrix	brain
30	chr12:21591600-21594800	Weak transcription	Colonic Mucosa	Colon
31	chr12:21591600-21594800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:21591600-21594800	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:21591600-21594800	Weak transcription	Pancreas	Pancrea
34	chr12:21591600-21598600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:21591600-21599600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:21591600-21609000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:21591600-21609000	Weak transcription	Brain Angular Gyrus	brain
38	chr12:21591600-21609200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:21591800-21592400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:21591800-21592400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:21591800-21592600	Enhancers	Liver	Liver
42	chr12:21591800-21592600	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr12:21591800-21592600	Enhancers	Thymus	Thymus
44	chr12:21591800-21592800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:21591800-21592800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:21591800-21593200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr12:21591800-21593400	Enhancers	Primary B cells from cord blood	blood
48	chr12:21591800-21593600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr12:21591800-21594200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr12:21591800-21594200	Weak transcription	Fetal Lung	lung

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