Variant report

Variant	rs10515301
Chromosome Location	chr5:99606693-99606694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10515299	1.00[ASN][1000 genomes]
rs12109873	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1504533	0.89[ASN][1000 genomes]
rs1628244	0.83[ASN][1000 genomes]
rs17140495	0.98[ASN][1000 genomes]
rs17141879	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17146499	0.93[ASN][1000 genomes]
rs17164539	0.98[ASN][1000 genomes]
rs1841979	0.83[ASN][1000 genomes]
rs2548206	0.83[ASN][1000 genomes]
rs2617324	0.83[ASN][1000 genomes]
rs4279311	1.00[ASN][1000 genomes]
rs56728498	0.96[ASN][1000 genomes]
rs59181522	0.96[ASN][1000 genomes]
rs72660709	0.92[ASN][1000 genomes]
rs72660710	0.98[ASN][1000 genomes]
rs72660711	1.00[ASN][1000 genomes]
rs72660722	0.93[ASN][1000 genomes]
rs73776474	0.87[AFR][1000 genomes]
rs766692	0.83[ASN][1000 genomes]
rs766693	0.83[ASN][1000 genomes]
rs794990	0.83[ASN][1000 genomes]
rs794992	0.83[ASN][1000 genomes]
rs794993	0.83[ASN][1000 genomes]
rs795672	0.82[ASN][1000 genomes]
rs795674	0.82[ASN][1000 genomes]
rs795677	0.82[ASN][1000 genomes]
rs795679	0.82[ASN][1000 genomes]
rs795681	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:42 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758006	chr5:99207674-99846255	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	esv2759359	chr5:99207674-99883371	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	esv34624	chr5:99383469-99664527	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1807423	chr5:99385971-99635944	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv2757124	chr5:99424756-99883371	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1032625	chr5:99425442-99664628	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1020130	chr5:99428583-99683405	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv882446	chr5:99434080-99728990	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv882452	chr5:99438989-99669656	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1031968	chr5:99446627-99610086	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1034711	chr5:99446627-99662421	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv523868	chr5:99458306-99665423	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv599165	chr5:99469004-100063039	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv482414	chr5:99469092-99632939	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1025298	chr5:99477594-99662421	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv537823	chr5:99477594-99662421	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv427726	chr5:99501625-99635944	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv599166	chr5:99507580-99665423	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv1024587	chr5:99515368-99616504	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv432785	chr5:99522748-99614601	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv525989	chr5:99524263-99665423	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv1033936	chr5:99531518-99616504	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv1021223	chr5:99531518-99627127	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	lncRNA	1 gene(s)	inside rSNPs	diseases
24	nsv1030532	chr5:99531518-99634772	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS	lncRNA	1 gene(s)	inside rSNPs	diseases
25	nsv1031661	chr5:99532806-99616504	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	lncRNA	1 gene(s)	inside rSNPs	diseases
26	nsv599167	chr5:99533649-99608856	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	lncRNA	1 gene(s)	inside rSNPs	diseases
27	nsv432788	chr5:99534096-99614601	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	lncRNA	1 gene(s)	inside rSNPs	diseases
28	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
29	nsv882455	chr5:99534276-99720953	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
30	nsv432789	chr5:99536420-99772825	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
31	nsv1015788	chr5:99545369-99745835	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
32	nsv537824	chr5:99545369-99745835	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
33	nsv1020273	chr5:99545369-99779031	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
34	nsv432790	chr5:99555492-99644635	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	lncRNA	1 gene(s)	inside rSNPs	diseases
35	nsv968843	chr5:99558009-99615244	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	lncRNA	1 gene(s)	inside rSNPs	diseases
36	nsv599168	chr5:99558792-99745767	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
37	esv2763875	chr5:99581111-99843423	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
38	nsv599169	chr5:99581379-99665423	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
39	nsv432791	chr5:99581524-99755077	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
40	nsv882457	chr5:99596369-99669656	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
41	nsv599170	chr5:99606651-99656681	Weak transcription Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
42	nsv882458	chr5:99606693-99848334	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10515301	LIX1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:99604200-99607200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:99604200-99607400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:99605800-99606800	Enhancers	Primary hematopoietic stem cells	blood
4	chr5:99605800-99606800	Enhancers	Fetal Brain Male	brain
5	chr5:99605800-99606800	Enhancers	Fetal Kidney	kidney
6	chr5:99606000-99606800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:99606000-99606800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:99606000-99607600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr5:99606000-99607800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr5:99606200-99606800	Enhancers	Fetal Lung	lung
11	chr5:99606400-99606800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr5:99606400-99607200	Enhancers	HUVEC	blood vessel
13	chr5:99606600-99606800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:99606600-99609200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:99606600-99609600	Weak transcription	NHEK	skin

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