Variant report

Variant	rs1949411
Chromosome Location	chr2:63571808-63571809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11125961	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11680079	1.00[JPT][hapmap]
rs11683229	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[ASN][1000 genomes]
rs11685079	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11893120	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11900732	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12993094	0.84[ASN][1000 genomes]
rs13000175	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs13013890	0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs13021852	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13028634	0.80[ASN][1000 genomes]
rs13030917	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13431584	0.84[CHB][hapmap];0.83[YRI][hapmap]
rs1446568	0.92[CHB][hapmap]
rs17027650	0.82[LWK][hapmap];0.83[YRI][hapmap]
rs17027651	0.81[CHB][hapmap]
rs17027692	0.83[YRI][hapmap]
rs1852909	1.00[YRI][hapmap]
rs2166498	0.92[CHB][hapmap]
rs2421917	0.80[LWK][hapmap];0.85[YRI][hapmap]
rs2421918	0.86[LWK][hapmap];0.83[YRI][hapmap]
rs2421919	0.80[LWK][hapmap]
rs33977056	0.92[ASW][hapmap];0.92[CHB][hapmap];0.88[GIH][hapmap]
rs35684492	0.90[ASN][1000 genomes]
rs6704998	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7595595	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv535768	chr2:63413596-63631407	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1009191	chr2:63473443-63578508	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv834241	chr2:63490262-63668205	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1014935	chr2:63545598-63599535	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1012628	chr2:63545598-63604859	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1013613	chr2:63545598-63606689	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1949411	NAPA	trans	cerebellum	SCAN
rs1949411	CEP68	cis	parietal	SCAN
rs1949411	OTX1	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63553000-63573600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:63563800-63573000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:63567800-63585600	Weak transcription	Gastric	stomach
4	chr2:63570000-63572000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:63570800-63572800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:63571200-63572000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
7	chr2:63571400-63572000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
8	chr2:63571400-63572000	ZNF genes & repeats	Left Ventricle	heart
9	chr2:63571400-63572200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:63571400-63572200	Enhancers	HMEC	breast
11	chr2:63571400-63572600	ZNF genes & repeats	Aorta	Aorta
12	chr2:63571400-63572600	ZNF genes & repeats	Liver	Liver
13	chr2:63571400-63572600	ZNF genes & repeats	Ovary	ovary
14	chr2:63571600-63572600	ZNF genes & repeats	Colon Smooth Muscle	Colon
15	chr2:63571600-63572600	Enhancers	NHEK	skin
16	chr2:63571600-63573400	Enhancers	Fetal Heart	heart
17	chr2:63571600-63574000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr2:63571800-63572000	Enhancers	Psoas Muscle	Psoas
19	chr2:63571800-63572200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr2:63571800-63573600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:63571800-63577600	Weak transcription	Primary B cells from cord blood	blood
22	chr2:63571800-63580800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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