Variant report

Variant	rs4658269
Chromosome Location	chr1:92247654-92247655
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:92245858..92248144-chr1:92269665..92271280,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10493859	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[TSI][hapmap]
rs11578569	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs11804539	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12118714	0.84[EUR][1000 genomes]
rs12123363	1.00[CHB][hapmap]
rs12751910	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473768	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556192	1.00[CHB][hapmap]
rs17443164	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2810884	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[TSI][hapmap]
rs284188	1.00[JPT][hapmap]
rs284201	1.00[JPT][hapmap]
rs4658114	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658265	1.00[JPT][hapmap]
rs4658270	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs4658273	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[TSI][hapmap]
rs6604052	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604053	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71650466	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv519291	chr1:92240685-92248695	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4658269	PKN2	cis	cerebellum	SCAN
rs4658269	LRRC8D	cis	cerebellum	SCAN
rs4658269	GFI1	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92217800-92247800	Weak transcription	Small Intestine	intestine
2	chr1:92220600-92255800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:92221000-92248000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:92227000-92257200	Weak transcription	Fetal Intestine Small	intestine
5	chr1:92230600-92247800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:92233200-92257000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:92235600-92247800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:92238600-92249400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:92241200-92249000	Strong transcription	HepG2	liver
10	chr1:92241400-92255800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:92241800-92248000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:92241800-92255800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:92242600-92248000	Weak transcription	Aorta	Aorta
14	chr1:92242600-92248400	Enhancers	Fetal Lung	lung
15	chr1:92242800-92249800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:92243400-92248400	Weak transcription	Esophagus	oesophagus
17	chr1:92243600-92250200	Weak transcription	Psoas Muscle	Psoas
18	chr1:92243800-92247800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:92243800-92247800	Weak transcription	Liver	Liver
20	chr1:92244000-92253600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:92244200-92248000	Enhancers	Fetal Muscle Leg	muscle
22	chr1:92244600-92248800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:92244600-92255200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:92244600-92257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:92244800-92248400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:92244800-92251000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr1:92245000-92249200	Genic enhancers	Fetal Stomach	stomach
28	chr1:92245200-92248000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:92245200-92261200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:92245400-92254200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:92245600-92247800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:92245600-92247800	Weak transcription	Left Ventricle	heart
33	chr1:92245600-92247800	Weak transcription	Right Atrium	heart
34	chr1:92245600-92254000	Weak transcription	Brain Anterior Caudate	brain
35	chr1:92245600-92258400	Weak transcription	Brain Angular Gyrus	brain
36	chr1:92245800-92255200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:92246000-92247800	Enhancers	NHLF	lung
38	chr1:92246000-92248200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:92246000-92255400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:92246200-92250600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr1:92246200-92250600	Enhancers	Colon Smooth Muscle	Colon
42	chr1:92246200-92251000	Enhancers	HUVEC	blood vessel
43	chr1:92246400-92247800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:92246400-92248400	Enhancers	Fetal Muscle Trunk	muscle
45	chr1:92246400-92248600	Genic enhancers	Stomach Smooth Muscle	stomach
46	chr1:92246400-92248800	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:92246400-92249000	Enhancers	Fetal Heart	heart
48	chr1:92246400-92249400	Enhancers	Ovary	ovary
49	chr1:92246400-92250000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr1:92246600-92247800	Enhancers	NH-A	brain

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