Variant report

Variant	rs6449190
Chromosome Location	chr4:15796333-15796334
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10805347	0.90[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16892304	1.00[YRI][hapmap]
rs2286880	1.00[YRI][hapmap]
rs3756241	0.84[ASN][1000 genomes]
rs3775954	0.86[ASN][1000 genomes]
rs3796863	0.82[JPT][hapmap]
rs4425367	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4516711	0.82[JPT][hapmap]
rs4698420	0.82[JPT][hapmap]
rs6449180	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6831585	0.86[JPT][hapmap]
rs6836946	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6840069	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6841880	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9291638	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv10460	chr4:15757611-15818206	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1013204	chr4:15762970-15836237	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1010597	chr4:15776181-15836237	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6449190	C1QTNF7	cis	cerebellum	SCAN
rs6449190	FAM184B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15786400-15807400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:15794000-15812200	Genic enhancers	Dnd41	blood
3	chr4:15795200-15797400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:15795200-15797600	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr4:15795400-15797600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr4:15795600-15796800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr4:15795800-15797000	Enhancers	GM12878-XiMat	blood
8	chr4:15795800-15797400	Enhancers	Primary T cells from cord blood	blood
9	chr4:15796000-15796600	Weak transcription	Primary B cells from cord blood	blood
10	chr4:15796000-15797800	Enhancers	Primary hematopoietic stem cells	blood
11	chr4:15796000-15799200	Weak transcription	Psoas Muscle	Psoas
12	chr4:15796000-15800000	Weak transcription	Fetal Brain Male	brain
13	chr4:15796000-15800800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:15796000-15801200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:15796000-15805000	Weak transcription	Thymus	Thymus
16	chr4:15796000-15808200	Weak transcription	Spleen	Spleen
17	chr4:15796200-15796400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:15796200-15797000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr4:15796200-15804200	Weak transcription	Fetal Thymus	thymus

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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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