Variant report

Variant	rs4641331
Chromosome Location	chr1:172039455-172039456
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10752861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911275	0.82[CEU][hapmap]
rs12090953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2761184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2761185	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2761186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2761187	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2761190	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2819531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28378748	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4244191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916418	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs58503720	0.81[ASN][1000 genomes]
rs6425637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6665598	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	nsv3532	chr1:171997451-172042351	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4641331	CD3D	trans	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172010600-172051400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:172015000-172042600	Weak transcription	Fetal Brain Female	brain
3	chr1:172020200-172040600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:172024600-172040400	Weak transcription	Brain Anterior Caudate	brain
5	chr1:172024800-172040600	Weak transcription	Brain Germinal Matrix	brain
6	chr1:172025200-172040600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:172035800-172040400	Weak transcription	Left Ventricle	heart
8	chr1:172037600-172041400	Enhancers	Brain Cingulate Gyrus	brain
9	chr1:172037800-172041200	Enhancers	Brain Substantia Nigra	brain
10	chr1:172037800-172041800	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr1:172038200-172040400	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:172038200-172055400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:172038200-172058800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:172038800-172040600	Enhancers	Brain Angular Gyrus	brain
15	chr1:172038800-172042000	Enhancers	Fetal Stomach	stomach
16	chr1:172039000-172041800	Enhancers	Ovary	ovary
17	chr1:172039200-172041800	Weak transcription	Spleen	Spleen
18	chr1:172039400-172040400	Weak transcription	Fetal Kidney	kidney
19	chr1:172039400-172040600	Weak transcription	Brain Hippocampus Middle	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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