Variant report

Variant	rs6541166
Chromosome Location	chr1:221069370-221069371
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10495153	1.00[ASN][1000 genomes]
rs10495154	1.00[ASN][1000 genomes]
rs12565509	0.98[ASN][1000 genomes]
rs1572384	0.84[YRI][hapmap]
rs17009037	0.94[ASN][1000 genomes]
rs2784273	1.00[ASW][hapmap];0.86[MEX][hapmap];0.84[YRI][hapmap]
rs2807861	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2807866	0.86[ASW][hapmap];0.86[MEX][hapmap]
rs35014198	0.99[ASN][1000 genomes]
rs3820355	0.92[ASN][1000 genomes]
rs6678259	0.99[ASN][1000 genomes]
rs73108353	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519520	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs945447	0.90[ASN][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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv1798350	chr1:221020278-221069740	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6541166	KCTD3	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221066200-221070000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:221067400-221069800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:221067400-221069800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr1:221067400-221070400	Active TSS	Colon Smooth Muscle	Colon
5	chr1:221068200-221069600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:221068200-221069800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:221068200-221070200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:221068800-221069400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
9	chr1:221068800-221069400	Bivalent Enhancer	Fetal Stomach	stomach
10	chr1:221068800-221070000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr1:221068800-221070200	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr1:221069000-221069400	Bivalent Enhancer	Fetal Lung	lung
13	chr1:221069000-221069600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
14	chr1:221069000-221069600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
15	chr1:221069000-221079400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:221069200-221069400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
17	chr1:221069200-221069400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:221069200-221069400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
19	chr1:221069200-221069600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:221069200-221069800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
21	chr1:221069200-221069800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:221069200-221069800	Weak transcription	Spleen	Spleen
23	chr1:221069200-221070000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
24	chr1:221069200-221070000	Active TSS	Rectal Smooth Muscle	rectum
25	chr1:221069200-221070200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
26	chr1:221069200-221077400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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