Variant report

Variant	rs1396825
Chromosome Location	chr2:48463834-48463835
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48463548..48466435-chr2:48483353..48486334,2	K562	blood:
2	chr2:48457105..48459838-chr2:48462699..48465520,3	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1112259	0.80[MEX][hapmap]
rs11125166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4953555	1.00[JPT][hapmap]
rs58178746	0.80[AMR][1000 genomes]
rs922902	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs973894	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1005241	chr2:48413134-48493182	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2762552	chr2:48413146-48493182	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv457407	chr2:48414735-48493182	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv581774	chr2:48414735-48493182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1001850	chr2:48421389-48492090	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv535681	chr2:48421389-48492090	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1396825	FOXN2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48459600-48464800	Enhancers	HepG2	liver
2	chr2:48460600-48466000	Weak transcription	HMEC	breast
3	chr2:48461600-48464200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:48461800-48464800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:48461800-48464800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr2:48462000-48464400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr2:48462000-48464800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:48462400-48464200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:48462400-48464400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr2:48462600-48464400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr2:48463200-48464000	Enhancers	Primary hematopoietic stem cells	blood
12	chr2:48463200-48464200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr2:48463200-48464200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr2:48463200-48464200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:48463200-48464400	Enhancers	Fetal Intestine Large	intestine
16	chr2:48463200-48464800	Enhancers	Primary T cells from cord blood	blood
17	chr2:48463200-48464800	Enhancers	Fetal Intestine Small	intestine
18	chr2:48463400-48464000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr2:48463400-48464200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr2:48463400-48464200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr2:48463400-48464200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:48463400-48464200	Enhancers	HUVEC	blood vessel
23	chr2:48463600-48464000	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr2:48463600-48464000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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