Variant report

Variant	rs2506898
Chromosome Location	chr1:10604539-10604540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10604158..10605695-chr1:10610029..10612944,2	K562	blood:
2	chr1:10595945..10600298-chr1:10602356..10606682,5	K562	blood:

Variant related genes	Relation type
ENSG00000142655	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10157111	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10157119	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10746495	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779739	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10779743	0.96[ASN][1000 genomes]
rs10779744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10864461	0.89[EUR][1000 genomes]
rs10864463	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10864465	0.82[EUR][1000 genomes]
rs11121584	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11121585	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11121588	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11121589	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11121593	0.98[ASN][1000 genomes]
rs11121594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11121596	0.84[EUR][1000 genomes]
rs11121597	0.84[EUR][1000 genomes]
rs12033275	0.84[CEU][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs12128630	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12129678	0.84[EUR][1000 genomes]
rs12133103	0.95[ASN][1000 genomes]
rs12565494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12750901	0.91[ASN][1000 genomes]
rs12753364	0.98[ASN][1000 genomes]
rs17035156	0.95[GIH][hapmap]
rs2039175	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2039176	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2086650	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2183377	0.86[EUR][1000 genomes]
rs2480771	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2480772	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2480773	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2480775	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480780	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs2480781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2480786	0.90[GIH][hapmap]
rs2480787	0.85[EUR][1000 genomes]
rs2480789	1.00[GIH][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.81[EUR][1000 genomes]
rs2483678	0.95[GIH][hapmap]
rs2506878	0.83[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2506887	0.95[GIH][hapmap]
rs2506888	0.86[EUR][1000 genomes]
rs2506897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2506900	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2988398	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34230252	0.98[ASN][1000 genomes]
rs35409029	0.99[ASN][1000 genomes]
rs35612158	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240914	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs4240915	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4617401	0.88[ASN][1000 genomes]
rs4845936	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4846230	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4846231	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4846232	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4846233	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4846237	0.95[ASN][1000 genomes]
rs58788814	0.84[EUR][1000 genomes]
rs61777207	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61777208	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540937	0.98[ASN][1000 genomes]
rs6540938	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[ASN][1000 genomes]
rs6658073	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6661757	0.97[ASN][1000 genomes]
rs6663688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6663898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6664134	0.98[ASN][1000 genomes]
rs6681221	0.89[EUR][1000 genomes]
rs6687502	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6687622	0.98[ASN][1000 genomes]
rs6700023	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6700886	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs710130	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72641424	0.82[EUR][1000 genomes]
rs72641427	0.80[EUR][1000 genomes]
rs747124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7512467	0.84[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs7519424	0.99[ASN][1000 genomes]
rs7524790	0.91[ASN][1000 genomes]
rs7534954	0.94[ASN][1000 genomes]
rs7545184	0.85[EUR][1000 genomes]
rs944191	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9660006	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9661121	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv545395	chr1:10584672-10613660	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2506898	APITD1	cis	cerebellum	SCAN
rs2506898	VAMP3	cis	parietal	SCAN
rs2506898	PEX14	cis	multi-tissue	Pritchard
rs2506898	PEX14	cis	Lymphoblastoid	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10579400-10610200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:10589400-10664800	Weak transcription	Aorta	Aorta
3	chr1:10590200-10605200	Weak transcription	NHDF-Ad	bronchial
4	chr1:10591000-10639400	Weak transcription	Hela-S3	cervix
5	chr1:10591400-10609000	Weak transcription	Small Intestine	intestine
6	chr1:10591400-10629200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:10591600-10616000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:10592200-10615800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:10597200-10604800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:10598600-10621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:10599800-10608400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:10599800-10610000	Weak transcription	Stomach Mucosa	stomach
13	chr1:10600000-10608200	Weak transcription	Fetal Brain Male	brain
14	chr1:10600000-10615600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:10600000-10615800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:10600000-10619600	Weak transcription	Brain Substantia Nigra	brain
17	chr1:10600200-10614800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:10600200-10615800	Weak transcription	HSMM	muscle
19	chr1:10601000-10604600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr1:10601000-10607600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:10601000-10613000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:10601200-10613400	Weak transcription	Osteobl	bone
23	chr1:10601200-10619600	Weak transcription	Brain Anterior Caudate	brain
24	chr1:10601400-10604600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:10601400-10604600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:10601400-10610400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:10601400-10611000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:10601400-10611000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:10601400-10615600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:10601600-10607000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:10601600-10607000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:10601800-10605400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:10601800-10610000	Weak transcription	Fetal Lung	lung
34	chr1:10601800-10610000	Weak transcription	A549	lung
35	chr1:10601800-10610000	Weak transcription	HUVEC	blood vessel
36	chr1:10601800-10613200	Weak transcription	K562	blood
37	chr1:10601800-10613400	Weak transcription	Right Ventricle	heart
38	chr1:10602000-10606800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:10602000-10606800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:10602000-10607000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:10602000-10607000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:10602000-10607000	Weak transcription	Left Ventricle	heart
43	chr1:10602000-10607000	Weak transcription	Right Atrium	heart
44	chr1:10602000-10607200	Weak transcription	Pancreas	Pancrea
45	chr1:10602000-10608400	Weak transcription	Fetal Heart	heart
46	chr1:10602000-10609800	Weak transcription	Colonic Mucosa	Colon
47	chr1:10602000-10610000	Weak transcription	Gastric	stomach
48	chr1:10602000-10610200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:10602000-10610200	Weak transcription	HepG2	liver
50	chr1:10602000-10610600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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