Variant report

Variant	rs10225487
Chromosome Location	chr7:27860762-27860763
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10155851	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10267854	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10277437	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10486549	0.86[CEU][hapmap]
rs10486559	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10951184	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12666082	0.81[EUR][1000 genomes]
rs16874364	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16874393	0.86[CEU][hapmap]
rs16874395	0.86[CEU][hapmap]
rs17150563	0.83[EUR][1000 genomes]
rs17155537	0.86[CEU][hapmap]
rs17155702	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17155943	0.85[EUR][1000 genomes]
rs17155950	0.91[CEU][hapmap]
rs17155969	0.82[CEU][hapmap]
rs17155971	0.82[CEU][hapmap]
rs2051830	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2074579	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074769	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2107413	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2108309	0.94[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2158388	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237339	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2237340	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2237341	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2285931	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2299106	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2391450	0.82[CEU][hapmap]
rs2391488	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779473	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3940270	0.89[CEU][hapmap]
rs4719907	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4719908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4722741	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57932688	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58314651	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62449629	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62449639	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62449640	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62451077	0.85[EUR][1000 genomes]
rs62451079	0.84[EUR][1000 genomes]
rs62454806	0.87[EUR][1000 genomes]
rs62454945	0.86[EUR][1000 genomes]
rs6462048	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6462049	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6462052	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6462053	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6944251	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6944913	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6966984	0.84[YRI][hapmap]
rs6971813	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6972821	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72598505	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs759268	0.91[CEU][hapmap]
rs7784038	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7801301	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7803019	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7803227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7809735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9639563	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv5677	chr7:27839504-27884505	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1018550	chr7:27844038-27925645	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	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
rs10225487	PRR15	cis	parietal	SCAN
rs10225487	SNX10	cis	cerebellum	SCAN
rs10225487	KCNA2	trans	parietal	SCAN
rs10225487	SCRN1	cis	cerebellum	SCAN
rs10225487	CRHR2	cis	parietal	SCAN
rs10225487	TAX1BP1	cis	cerebellum	SCAN
rs10225487	HOXA13	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27781000-27861800	Weak transcription	Aorta	Aorta
2	chr7:27784800-27878400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:27798600-27874000	Weak transcription	Brain Angular Gyrus	brain
4	chr7:27806000-27882600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:27806400-27878600	Weak transcription	Right Ventricle	heart
6	chr7:27815600-27874000	Weak transcription	Pancreas	Pancrea
7	chr7:27823800-27878000	Weak transcription	Spleen	Spleen
8	chr7:27824200-27876800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:27825600-27874000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:27826000-27870000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:27827000-27881800	Weak transcription	Small Intestine	intestine
12	chr7:27827600-27878400	Weak transcription	Fetal Kidney	kidney
13	chr7:27834400-27873600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr7:27835200-27878200	Weak transcription	Gastric	stomach
15	chr7:27836400-27867400	Weak transcription	HUVEC	blood vessel
16	chr7:27836400-27878000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:27836400-27882200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:27837000-27873800	Weak transcription	Psoas Muscle	Psoas
19	chr7:27840000-27880600	Weak transcription	Hela-S3	cervix
20	chr7:27842400-27877800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:27843600-27877000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:27847600-27885200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr7:27848400-27871600	Weak transcription	HMEC	breast
24	chr7:27848400-27873400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:27848600-27868200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr7:27848600-27871000	Weak transcription	K562	blood
27	chr7:27849200-27873400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr7:27850200-27881400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr7:27850400-27861200	Strong transcription	Placenta	Placenta
30	chr7:27851200-27863800	Strong transcription	Liver	Liver
31	chr7:27851400-27860800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:27852200-27862600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr7:27853000-27868800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:27853200-27861000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr7:27853400-27864000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:27853600-27862000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:27853800-27861200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:27854200-27861600	Weak transcription	Fetal Heart	heart
39	chr7:27854200-27864000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:27854200-27882200	Weak transcription	Brain Substantia Nigra	brain
41	chr7:27855200-27863800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:27855600-27860800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr7:27855600-27862000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr7:27855600-27863400	Strong transcription	Primary hematopoietic stem cells	blood
45	chr7:27855600-27864200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr7:27856000-27862000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:27856000-27882200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr7:27856600-27866000	Weak transcription	Fetal Intestine Small	intestine
49	chr7:27856600-27874000	Weak transcription	Fetal Stomach	stomach
50	chr7:27856800-27862000	Weak transcription	Thymus	Thymus

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