Variant report

Variant	rs2162480
Chromosome Location	chr2:231130887-231130888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13403849	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405136	0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1559909	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16827035	0.82[CHB][hapmap]
rs2303542	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34304229	0.80[ASN][1000 genomes]
rs3754938	0.82[ASN][1000 genomes]
rs3769845	0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs56317957	0.81[ASN][1000 genomes]
rs58989813	0.99[ASN][1000 genomes]
rs62191185	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6707578	0.82[CHB][hapmap]
rs6708227	0.80[ASN][1000 genomes]
rs6717938	0.80[ASN][1000 genomes]
rs6734941	0.85[ASN][1000 genomes]
rs7557737	0.88[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7582543	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers 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	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2162480	PSMD1	cis	parietal	SCAN
rs2162480	INPP5D	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231090200-231170000	Weak transcription	Spleen	Spleen
2	chr2:231119200-231141200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:231120600-231134200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr2:231125400-231136800	Strong transcription	Primary B cells from cord blood	blood
5	chr2:231127800-231135400	Weak transcription	Primary T cells from cord blood	blood
6	chr2:231128000-231131000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr2:231128200-231135600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:231128200-231166000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:231128600-231133800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:231128600-231134000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:231128600-231134200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:231128600-231134800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:231129000-231135000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:231129400-231131400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:231129400-231131600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:231129400-231137200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:231129600-231131600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:231129800-231140800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:231130000-231138200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:231130200-231131800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:231130200-231137800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr2:231130600-231131800	Genic enhancers	GM12878-XiMat	blood

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