Variant report

Variant	rs3738364
Chromosome Location	chr1:224872443-224872444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10158430	0.82[EUR][1000 genomes]
rs10458376	0.82[EUR][1000 genomes]
rs10495223	1.00[CEU][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10495224	1.00[CEU][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10799276	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10915689	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10915692	0.83[ASW][hapmap];0.81[CEU][hapmap];0.83[LWK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12030079	0.80[CEU][hapmap]
rs12030696	0.81[CEU][hapmap]
rs12032349	0.81[CEU][hapmap]
rs12041370	0.81[CEU][hapmap]
rs12046028	0.88[ASW][hapmap];0.81[CEU][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12118224	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12123347	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs12133496	1.00[CEU][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12133529	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12134264	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12135077	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12144488	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12145463	0.94[CEU][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs16851528	1.00[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17514252	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs17514370	0.82[EUR][1000 genomes]
rs17573714	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs298736	0.81[CEU][hapmap]
rs3738363	0.88[ASW][hapmap];0.81[CEU][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3738365	0.88[ASW][hapmap];0.81[CEU][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4564105	0.81[CEU][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56365526	0.81[EUR][1000 genomes]
rs58158731	0.92[EUR][1000 genomes]
rs6426145	1.00[CEU][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6426146	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6665737	0.82[EUR][1000 genomes]
rs6666840	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6666853	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6666929	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6676362	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6676444	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs722849	0.81[CEU][hapmap];0.91[LWK][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7521221	0.81[CEU][hapmap]
rs7525096	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7537218	0.82[EUR][1000 genomes]
rs7547239	0.81[CEU][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7549891	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs930323	0.81[CEU][hapmap];0.91[LWK][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9660759	0.81[CEU][hapmap]
rs9661696	0.81[CEU][hapmap]
rs9661955	0.81[CEU][hapmap]
rs9662190	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3738364	CNIH4	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224832200-224884400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:224833200-224874400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:224858400-224874200	Weak transcription	NH-A	brain
4	chr1:224861200-224876800	Weak transcription	Ovary	ovary
5	chr1:224862400-224902000	Weak transcription	Pancreas	Pancrea
6	chr1:224864000-224876200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:224868000-224874000	Weak transcription	Gastric	stomach
8	chr1:224868400-224875200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:224869400-224872600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:224869800-224877200	Weak transcription	Dnd41	blood
11	chr1:224870200-224872600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:224871200-224873000	Enhancers	Fetal Brain Male	brain
13	chr1:224871400-224876400	Strong transcription	NHDF-Ad	bronchial
14	chr1:224871600-224872800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:224871600-224873000	Enhancers	Brain Germinal Matrix	brain
16	chr1:224871800-224872800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:224871800-224872800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:224871800-224873000	Strong transcription	NHLF	lung
19	chr1:224871800-224884600	Weak transcription	Fetal Brain Female	brain
20	chr1:224872000-224872600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr1:224872000-224873400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:224872000-224874600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:224872400-224872600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:224872400-224873200	Enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links