Variant report

Variant	rs10490895
Chromosome Location	chr3:85081790-85081791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11127870	0.83[ASN][1000 genomes]
rs11127871	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs11127872	0.83[ASN][1000 genomes]
rs12163548	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs12486854	0.83[ASN][1000 genomes]
rs12490121	0.82[CHB][hapmap]
rs12494141	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs12495099	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs12496044	0.83[ASN][1000 genomes]
rs12497566	0.83[ASN][1000 genomes]
rs17022171	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs17022259	1.00[ASW][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs17022281	1.00[ASW][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs17022298	0.83[ASN][1000 genomes]
rs1872557	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1872558	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs450495	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs7649296	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs9870384	0.82[CHD][hapmap]

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	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3419993	chr3:85030343-85663403	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv492289	chr3:85066623-85319147	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2753915	chr3:85071410-85624810	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85065200-85082200	Weak transcription	Brain Hippocampus Middle	brain
2	chr3:85068600-85090600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:85071400-85082400	Weak transcription	Fetal Brain Female	brain
4	chr3:85071600-85082000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:85078800-85081800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:85079600-85083200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:85079600-85083600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:85079600-85086400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:85079800-85082200	Weak transcription	Psoas Muscle	Psoas
10	chr3:85080000-85082200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:85080000-85082800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:85080000-85083400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:85080400-85082400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:85080400-85082800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:85081400-85082200	Enhancers	Brain Angular Gyrus	brain
16	chr3:85081400-85082200	Enhancers	Brain Anterior Caudate	brain
17	chr3:85081400-85088800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:85081600-85082000	Weak transcription	Cortex derived primary cultured neurospheres	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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