Variant report

Variant	rs9503893
Chromosome Location	chr6:4031998-4031999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs12174184	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408457	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543355	0.91[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1969837	0.82[EUR][1000 genomes]
rs2181894	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2745451	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2745452	0.87[CEU][hapmap]
rs3747761	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747763	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761787	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4466281	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959916	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959918	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4959919	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6900476	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905475	0.83[ASN][1000 genomes]
rs6906467	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[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910519	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914180	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916982	0.95[ASN][1000 genomes]
rs6921738	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6924389	0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6930892	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933593	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6939049	1.00[JPT][hapmap]
rs6941706	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs697745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707984	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707987	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs707988	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73349780	0.84[ASN][1000 genomes]
rs7744603	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7763233	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853396	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs853397	0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs853398	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs853399	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853400	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853402	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853403	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853404	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853407	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853409	0.81[ASN][1000 genomes]
rs853410	0.83[ASN][1000 genomes]
rs853411	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs860477	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860478	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9328215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328216	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9405217	0.84[CEU][hapmap]
rs9405693	0.91[CEU][hapmap]
rs9405694	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941443	0.95[ASN][1000 genomes]
rs942474	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
4	nsv1034223	chr6:4030708-4060347	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9503893	PECI	cis	parietal	SCAN
rs9503893	PECI	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4022400-4043400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:4022600-4049400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:4023000-4032000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:4023000-4038600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:4023000-4063600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:4023200-4034000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr6:4023200-4035600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:4023200-4043400	Weak transcription	Aorta	Aorta
9	chr6:4023200-4064000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:4023400-4038800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:4023400-4040600	Weak transcription	Fetal Brain Male	brain
12	chr6:4023400-4071600	Weak transcription	Stomach Mucosa	stomach
13	chr6:4023800-4032000	Weak transcription	Fetal Lung	lung
14	chr6:4023800-4032200	Weak transcription	Colonic Mucosa	Colon
15	chr6:4023800-4033600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:4023800-4037400	Weak transcription	Fetal Brain Female	brain
17	chr6:4023800-4037600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:4023800-4067000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:4024000-4035600	Weak transcription	NHLF	lung
20	chr6:4024000-4036400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:4024000-4037600	Weak transcription	HSMMtube	muscle
22	chr6:4024200-4037000	Weak transcription	Right Atrium	heart
23	chr6:4024200-4040200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:4024400-4035800	Weak transcription	Thymus	Thymus
25	chr6:4024600-4032000	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:4024600-4036600	Weak transcription	Spleen	Spleen
27	chr6:4024600-4040200	Weak transcription	Esophagus	oesophagus
28	chr6:4024600-4059200	Strong transcription	Fetal Thymus	thymus
29	chr6:4025200-4039200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:4025400-4037600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:4025800-4034000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:4026000-4032000	Weak transcription	Adipose Nuclei	Adipose
33	chr6:4026000-4032800	Weak transcription	Brain Anterior Caudate	brain
34	chr6:4027000-4032200	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:4027000-4033400	Genic enhancers	Primary T cells from cord blood	blood
36	chr6:4027000-4034200	Genic enhancers	Dnd41	blood
37	chr6:4027200-4038200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr6:4027200-4058200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr6:4027400-4032000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:4027400-4032000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:4027400-4032600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:4027400-4037600	Weak transcription	Left Ventricle	heart
43	chr6:4027400-4039600	Weak transcription	Fetal Heart	heart
44	chr6:4027400-4039600	Weak transcription	Gastric	stomach
45	chr6:4027800-4040800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:4027800-4041600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:4028200-4035000	Strong transcription	NHEK	skin
48	chr6:4028200-4038800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:4028600-4039000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:4028800-4035800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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