Variant report

Variant	rs12653926
Chromosome Location	chr5:151250248-151250249
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10044368	0.88[CHB][hapmap]
rs10062169	0.84[ASN][1000 genomes]
rs10078632	0.80[ASN][1000 genomes]
rs10079787	0.80[ASN][1000 genomes]
rs1042877	0.88[CHB][hapmap]
rs10463320	0.81[ASN][1000 genomes]
rs1062177	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs11167559	0.82[ASN][1000 genomes]
rs12108921	0.94[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs12109022	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs12109585	0.80[ASN][1000 genomes]
rs12515762	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12518238	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518722	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12522670	0.84[CEU][hapmap]
rs12654573	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1346489	0.97[EUR][1000 genomes]
rs1366238	0.82[ASN][1000 genomes]
rs1428159	0.84[ASN][1000 genomes]
rs1428160	0.84[ASN][1000 genomes]
rs1433041	0.88[CHB][hapmap]
rs1549622	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1549920	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs17741826	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs17804178	0.83[EUR][1000 genomes]
rs2033212	0.82[ASN][1000 genomes]
rs2347596	0.81[EUR][1000 genomes]
rs2347597	0.88[CHB][hapmap]
rs2913878	0.80[ASN][1000 genomes]
rs2913879	0.82[ASN][1000 genomes]
rs2913881	0.84[ASN][1000 genomes]
rs2913882	0.80[ASN][1000 genomes]
rs2913888	0.84[ASN][1000 genomes]
rs2913889	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs2913892	0.94[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs2913893	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs2913894	0.94[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2915822	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs2915826	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2915827	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2915868	0.88[CHB][hapmap]
rs2915872	0.88[CHB][hapmap]
rs2915876	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap]
rs2915878	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2915879	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2915880	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2915882	1.00[CEU][hapmap]
rs2915886	0.82[CHB][hapmap]
rs2915887	0.83[EUR][1000 genomes]
rs2915888	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2915890	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2964570	0.88[CHB][hapmap]
rs2964574	0.90[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs2964584	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2964587	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2964591	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2964592	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs2964597	0.82[ASN][1000 genomes]
rs2964599	0.87[ASN][1000 genomes]
rs2964601	0.84[ASN][1000 genomes]
rs2964603	0.84[ASN][1000 genomes]
rs2964604	0.84[ASN][1000 genomes]
rs2964606	0.84[ASN][1000 genomes]
rs2964612	0.83[EUR][1000 genomes]
rs4075273	0.80[ASN][1000 genomes]
rs4076138	0.80[ASN][1000 genomes]
rs4259159	0.84[ASN][1000 genomes]
rs4331885	0.87[ASN][1000 genomes]
rs4478307	0.84[ASN][1000 genomes]
rs4571461	0.88[CHB][hapmap]
rs59580263	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62377945	0.85[EUR][1000 genomes]
rs62394146	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62394155	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62395861	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6579897	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6868371	0.80[ASN][1000 genomes]
rs6878691	0.80[ASN][1000 genomes]
rs6884630	0.97[EUR][1000 genomes]
rs6892117	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6896518	0.80[ASN][1000 genomes]
rs6896664	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72802204	0.81[EUR][1000 genomes]
rs72802219	0.84[ASN][1000 genomes]
rs7711609	0.80[ASN][1000 genomes]
rs7711771	0.80[ASN][1000 genomes]
rs7712779	0.83[ASN][1000 genomes]
rs7719617	0.88[CHB][hapmap]
rs7725327	0.80[ASN][1000 genomes]
rs7728956	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs7729026	0.82[ASN][1000 genomes]
rs7733241	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs7734314	0.88[CHB][hapmap]
rs892005	0.81[EUR][1000 genomes]
rs892006	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs919262	0.97[EUR][1000 genomes]
rs919263	0.97[EUR][1000 genomes]
rs9324712	0.80[ASN][1000 genomes]
rs9324714	0.87[ASN][1000 genomes]
rs973529	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1808837	chr5:151238149-151260215	Enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv1807514	chr5:151242208-151252867	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv1807896	chr5:151242208-151252867	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv1808791	chr5:151242208-151252867	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1808872	chr5:151242208-151252867	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3487128	chr5:151247859-151254357	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3471109	chr5:151248159-151252657	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3487127	chr5:151248309-151254207	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv3487129	chr5:151248309-151254207	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv11199	chr5:151249350-151252921	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
11	esv1805240	chr5:151249408-151252867	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
12	esv1807490	chr5:151249408-151252867	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
13	esv1808128	chr5:151249408-151252867	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
14	esv1811714	chr5:151249408-151252867	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
15	esv1812706	chr5:151249408-151252867	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
16	esv1813297	chr5:151249408-151252867	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
17	esv3471110	chr5:151249859-151252657	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
18	esv3471107	chr5:151249859-151254957	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
19	esv1805196	chr5:151250248-151252867	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
20	esv1806540	chr5:151250248-151252867	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
21	esv1808206	chr5:151250248-151252867	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
22	esv1809796	chr5:151250248-151252867	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
23	esv1810176	chr5:151250248-151252867	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
24	esv1811127	chr5:151250248-151252867	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
25	esv1811556	chr5:151250248-151252867	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
26	esv1813291	chr5:151250248-151252867	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12653926	RP11-54C4.1	cis	Nerve Tibial	GTEx
rs12653926	RP11-54C4.1	cis	Thyroid	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151235200-151264200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:151249800-151250800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:151249800-151250800	Enhancers	HSMM	muscle
4	chr5:151249800-151251000	Enhancers	HSMMtube	muscle
5	chr5:151249800-151251200	Enhancers	NHDF-Ad	bronchial
6	chr5:151250000-151250400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:151250000-151250800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:151250000-151250800	Enhancers	NH-A	brain
9	chr5:151250000-151250800	Enhancers	Osteobl	bone
10	chr5:151250000-151251000	Enhancers	HMEC	breast
11	chr5:151250000-151251800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr5:151250000-151252200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:151250200-151250600	Enhancers	NHLF	lung
14	chr5:151250200-151250800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:151250200-151250800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:151250200-151250800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:151250200-151250800	Enhancers	NHEK	skin

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