Variant report

Variant	rs1341573
Chromosome Location	chr1:74896816-74896817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1022915	1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs10890127	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.92[ASN][1000 genomes]
rs10890128	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11210457	0.91[ASN][1000 genomes]
rs11210458	0.83[CHB][hapmap];0.92[JPT][hapmap];0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11210463	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs12048736	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1325605	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1325606	0.83[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1527684	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2203369	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.92[ASN][1000 genomes]
rs274581	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs3765670	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6665693	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs6703217	0.92[ASN][1000 genomes]
rs699844	0.92[CHB][hapmap];0.81[CHD][hapmap]
rs7515072	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.92[ASN][1000 genomes]
rs7517774	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs925643	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522147	chr1:74338530-74983835	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1003171	chr1:74407468-75122270	Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv535000	chr1:74407468-75122270	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1011308	chr1:74545016-74932777	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1007414	chr1:74726454-74976335	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv535002	chr1:74726454-74976335	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1010042	chr1:74798856-75001977	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1002903	chr1:74831209-74993866	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1341573	TNNI3K	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:74878600-74898800	Weak transcription	Left Ventricle	heart
2	chr1:74894400-74897400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:74894800-74897400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:74894800-74904600	Enhancers	Fetal Heart	heart
5	chr1:74895200-74897000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:74895800-74897600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:74896400-74897400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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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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