Variant report

Variant	rs12203688
Chromosome Location	chr6:33693624-33693625
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33692582..33695228-chr6:33717074..33719027,2	K562	blood:
2	chr6:33673686..33677249-chr6:33690275..33693823,3	K562	blood:
3	chr6:33692177..33695084-chr6:33755126..33757076,2	MCF-7	breast:
4	chr6:33678200..33682184-chr6:33690933..33696225,5	K562	blood:
5	chr6:33693493..33694998-chr6:33697111..33699180,2	K562	blood:
6	chr6:33693249..33695267-chr6:33719623..33721316,2	K562	blood:

Variant related genes	Relation type
ENSG00000137288	Chromatin interaction
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10456075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947415	0.84[CEU][hapmap]
rs10947426	0.87[AFR][1000 genomes]
rs10947427	0.83[GIH][hapmap]
rs10947432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947441	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs11757379	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs12153870	0.87[AFR][1000 genomes]
rs12189725	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12190155	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12192035	0.85[ASN][1000 genomes]
rs12193658	0.84[EUR][1000 genomes]
rs12195707	0.84[CEU][hapmap];0.87[AFR][1000 genomes]
rs12199132	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12205398	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205667	0.87[AFR][1000 genomes]
rs12207382	0.85[JPT][hapmap]
rs12211490	1.00[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.88[ASN][1000 genomes]
rs12211554	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs12211565	0.88[ASN][1000 genomes]
rs12214669	1.00[LWK][hapmap]
rs12215329	0.88[ASN][1000 genomes]
rs12660955	0.88[ASN][1000 genomes]
rs12661400	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662447	0.84[EUR][1000 genomes]
rs13200063	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs13203745	1.00[LWK][hapmap];0.95[MKK][hapmap]
rs13204162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204975	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13206228	0.88[ASN][1000 genomes]
rs13207666	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13213889	0.83[ASN][1000 genomes]
rs13214874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13220421	0.87[AFR][1000 genomes]
rs2274459	1.00[ASW][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs2281831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281917	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2281918	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2281919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296737	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2296749	0.88[ASN][1000 genomes]
rs34139049	0.94[ASN][1000 genomes]
rs34339105	0.88[ASN][1000 genomes]
rs34472165	0.88[ASN][1000 genomes]
rs34517899	0.87[AFR][1000 genomes]
rs34778247	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs34869648	0.88[ASN][1000 genomes]
rs34884883	0.82[ASN][1000 genomes]
rs35088242	0.87[AFR][1000 genomes]
rs35095444	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35274562	0.94[ASN][1000 genomes]
rs35646598	0.94[ASN][1000 genomes]
rs35698850	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35721478	0.88[ASN][1000 genomes]
rs35797388	0.88[ASN][1000 genomes]
rs36097803	0.87[AFR][1000 genomes]
rs36122085	0.82[ASN][1000 genomes]
rs3793080	0.80[TSI][hapmap]
rs3806107	0.80[TSI][hapmap]
rs3818526	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3818532	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4559081	1.00[LWK][hapmap]
rs66670017	0.88[ASN][1000 genomes]
rs68168863	0.88[ASN][1000 genomes]
rs6925337	0.85[JPT][hapmap]
rs729376	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751095	0.88[ASN][1000 genomes]
rs755239	0.88[ASN][1000 genomes]
rs877187	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296097	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9469554	0.92[CEU][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12203688	ITPR3	cis	multi-tissue	Pritchard
rs12203688	LEMD2	cis	parietal	SCAN
rs12203688	C6orf125	cis	cerebellum	SCAN
rs12203688	LEMD2	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33680000-33695200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:33680000-33695800	Weak transcription	Spleen	Spleen
3	chr6:33680000-33696200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:33680000-33698400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:33680000-33705000	Weak transcription	Brain Angular Gyrus	brain
6	chr6:33686200-33700200	Weak transcription	Liver	Liver
7	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:33686600-33695800	Weak transcription	Right Atrium	heart
9	chr6:33686600-33698600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:33687400-33694000	Weak transcription	Brain Anterior Caudate	brain
11	chr6:33688800-33698200	Weak transcription	Lung	lung
12	chr6:33688800-33700000	Strong transcription	HSMM	muscle
13	chr6:33689200-33696800	Strong transcription	HSMMtube	muscle
14	chr6:33689400-33695000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:33689600-33694600	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr6:33689600-33696600	Enhancers	Fetal Brain Male	brain
17	chr6:33690600-33694200	Weak transcription	Placenta	Placenta
18	chr6:33690800-33708200	Weak transcription	Gastric	stomach
19	chr6:33691400-33694000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr6:33691600-33695600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:33691800-33694000	Weak transcription	Pancreas	Pancrea
22	chr6:33691800-33694400	Strong transcription	Left Ventricle	heart
23	chr6:33691800-33711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:33692000-33696800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:33692000-33697000	Weak transcription	Psoas Muscle	Psoas
26	chr6:33692000-33706800	Weak transcription	Fetal Intestine Small	intestine
27	chr6:33692000-33710200	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:33692600-33699200	Weak transcription	Fetal Lung	lung
29	chr6:33692800-33695600	Weak transcription	Brain Substantia Nigra	brain
30	chr6:33692800-33701000	Weak transcription	Fetal Brain Female	brain
31	chr6:33693000-33698600	Strong transcription	Brain Hippocampus Middle	brain
32	chr6:33693200-33694000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr6:33693200-33694000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr6:33693200-33694600	Genic enhancers	Right Ventricle	heart
35	chr6:33693200-33697200	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr6:33693200-33698200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr6:33693200-33700800	Strong transcription	Fetal Muscle Leg	muscle
38	chr6:33693400-33693800	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr6:33693400-33694400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:33693400-33695000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:33693400-33695200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:33693400-33701200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr6:33693600-33695000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr6:33693600-33712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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