Variant report

Variant	rs1529046
Chromosome Location	chr3:98252132-98252133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1461155	0.82[YRI][hapmap]
rs1461159	0.82[ASN][1000 genomes]
rs2091598	0.84[ASN][1000 genomes]
rs2230344	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35320048	0.82[ASN][1000 genomes]
rs4392455	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55707803	0.82[ASN][1000 genomes]
rs6799550	0.82[YRI][hapmap]
rs7430346	0.82[ASN][1000 genomes]
rs9819403	0.82[YRI][hapmap]
rs9833557	0.82[YRI][hapmap]
rs9834252	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528056	chr3:98101101-98317836	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv520503	chr3:98102801-98317836	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv834774	chr3:98108423-98274064	Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv834775	chr3:98170059-98367552	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv236502	chr3:98250046-98254624	Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1529046	IMPG2	cis	cerebellum	SCAN
rs1529046	ST3GAL6	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98250200-98256200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr3:98250600-98252400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:98250800-98252200	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr3:98250800-98252600	Active TSS	Colonic Mucosa	Colon
5	chr3:98250800-98253200	Active TSS	Primary T cells fromperipheralblood	blood
6	chr3:98250800-98253600	Active TSS	Duodenum Mucosa	Duodenum
7	chr3:98251000-98252200	Active TSS	Esophagus	oesophagus
8	chr3:98251000-98252400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:98251000-98252400	Active TSS	Sigmoid Colon	Sigmoid Colon
10	chr3:98251200-98252400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr3:98251600-98252400	Active TSS	Rectal Smooth Muscle	rectum
12	chr3:98251600-98257400	Active TSS	GM12878-XiMat	blood
13	chr3:98251800-98252400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:98252000-98252400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:98252000-98252600	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:98252000-98252600	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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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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