Variant report

Variant	rs2325704
Chromosome Location	chr1:158909164-158909165
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1633280	0.98[ASN][1000 genomes]
rs856080	0.97[AMR][1000 genomes];0.99[EUR][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	nsv1002401	chr1:158712627-158972031	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv872484	chr1:158863845-158909164	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv872485	chr1:158863845-158922287	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1007597	chr1:158874806-158934301	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv946443	chr1:158905154-158911493	Enhancers Weak transcription Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2325704	C1orf189	cis	cerebellum	SCAN
rs2325704	TPM3	cis	cerebellum	SCAN
rs2325704	GBAP1	cis	cerebellum	SCAN
rs2325704	KIRREL	cis	cerebellum	SCAN
rs2325704	CD5L	cis	cerebellum	SCAN
rs2325704	LOR	cis	cerebellum	SCAN
rs2325704	S100A6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158902200-158920000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:158904200-158912000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:158905600-158921800	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr1:158905600-158922000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:158905800-158930200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:158906600-158909600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:158906600-158919600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:158906800-158909400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:158906800-158910000	Strong transcription	Primary T cells from cord blood	blood
10	chr1:158907000-158909400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:158907000-158909600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:158907000-158919200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:158907200-158918200	Weak transcription	Primary B cells from cord blood	blood
14	chr1:158908000-158909200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:158908200-158910600	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:158908400-158912800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:158908800-158909600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:158909000-158909400	Enhancers	Primary T killer memory cells from peripheral blood	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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