Variant report

Variant	rs12026177
Chromosome Location	chr1:154137165-154137166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10158820	0.91[JPT][hapmap]
rs1044013	0.91[JPT][hapmap]
rs1113142	0.84[YRI][hapmap]
rs11265238	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11265251	0.91[JPT][hapmap]
rs11265425	0.95[JPT][hapmap]
rs11802893	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1194593	0.91[JPT][hapmap]
rs1194594	0.92[YRI][hapmap]
rs1194596	0.91[JPT][hapmap]
rs1194597	0.82[YRI][hapmap]
rs1194601	0.91[YRI][hapmap]
rs1194605	0.87[YRI][hapmap]
rs12025237	0.81[CEU][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs12026615	0.81[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12027999	0.80[EUR][1000 genomes]
rs12028949	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038362	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12043131	0.90[CEU][hapmap]
rs1205590	0.87[YRI][hapmap]
rs12062977	0.91[JPT][hapmap]
rs12733060	0.80[EUR][1000 genomes]
rs16835846	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16835852	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1685625	0.80[YRI][hapmap]
rs1760802	0.91[JPT][hapmap]
rs2274993	0.81[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs2340473	0.86[JPT][hapmap]
rs2500222	0.91[YRI][hapmap]
rs2633434	0.95[YRI][hapmap]
rs2790689	0.81[CEU][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap]
rs28372838	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879788	0.91[JPT][hapmap]
rs3002660	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34128679	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34335016	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35761479	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3762340	0.90[CEU][hapmap];0.95[JPT][hapmap]
rs3790613	0.81[CEU][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs3790614	0.80[EUR][1000 genomes]
rs3811453	0.90[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs3811455	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3828077	0.81[CEU][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs3935419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4433384	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4459102	0.81[CEU][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs4620534	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60282844	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6427509	0.91[JPT][hapmap]
rs6666943	0.84[YRI][hapmap]
rs6673752	0.81[CEU][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs6676022	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6719	0.91[JPT][hapmap]
rs715737	0.84[YRI][hapmap]
rs9803857	0.91[JPT][hapmap]

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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	nsv520398	chr1:154068196-154141908	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv872451	chr1:154101519-154139757	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12026177	DENND4B	cis	parietal	SCAN
rs12026177	HAX1	cis	cerebellum	SCAN
rs12026177	RAB13	cis	parietal	SCAN
rs12026177	PIP5K1A	cis	cerebellum	SCAN
rs12026177	SLC27A3	cis	lymphoblastoid	seeQTL
rs12026177	HAX1	cis	parietal	SCAN
rs12026177	HAX1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154112200-154138400	Weak transcription	Psoas Muscle	Psoas
2	chr1:154126400-154146000	Strong transcription	HMEC	breast
3	chr1:154127000-154143400	Strong transcription	Muscle Satellite Cultured Cells	--
4	chr1:154127000-154143600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:154127000-154148400	Strong transcription	Fetal Intestine Large	intestine
6	chr1:154127000-154149600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:154127200-154146000	Strong transcription	Fetal Brain Female	brain
8	chr1:154127400-154148200	Strong transcription	Liver	Liver
9	chr1:154127600-154148400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr1:154127800-154140200	Weak transcription	Pancreas	Pancrea
11	chr1:154127800-154150000	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr1:154128000-154148400	Strong transcription	Fetal Muscle Leg	muscle
13	chr1:154128000-154150400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:154128000-154150800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:154128200-154150200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:154128200-154151200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:154128400-154137200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:154128400-154137800	Weak transcription	Fetal Heart	heart
19	chr1:154128400-154146000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:154128400-154148400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:154128600-154146000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:154128600-154148600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:154129600-154143600	Strong transcription	HSMMtube	muscle
24	chr1:154129600-154145600	Strong transcription	HepG2	liver
25	chr1:154129600-154145600	Strong transcription	NHEK	skin
26	chr1:154129600-154149800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:154129600-154150400	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr1:154129800-154148200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr1:154130000-154148400	Strong transcription	HSMM	muscle
30	chr1:154130200-154145800	Strong transcription	Colonic Mucosa	Colon
31	chr1:154130200-154150600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:154130400-154137800	Strong transcription	Fetal Kidney	kidney
33	chr1:154130600-154138600	Strong transcription	Colon Smooth Muscle	Colon
34	chr1:154130600-154148000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr1:154130600-154148400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:154130600-154148400	Weak transcription	Right Atrium	heart
37	chr1:154130600-154149800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:154130600-154150000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:154130800-154148000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:154130800-154148600	Strong transcription	Osteobl	bone
41	chr1:154131000-154141600	Weak transcription	Fetal Brain Male	brain
42	chr1:154131000-154145800	Strong transcription	Hela-S3	cervix
43	chr1:154131400-154141600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr1:154131400-154148400	Strong transcription	Lung	lung
45	chr1:154131600-154137600	Weak transcription	Gastric	stomach
46	chr1:154131600-154143000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:154131600-154148000	Strong transcription	Primary B cells from cord blood	blood
48	chr1:154131600-154148400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:154131600-154148400	Strong transcription	Placenta	Placenta
50	chr1:154131600-154148800	Strong transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links