Variant report

Variant	rs2262771
Chromosome Location	chr4:48122948-48122949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48116908..48119075-chr4:48120990..48123464,3	K562	blood:
2	chr4:48121739..48123501-chr4:48126071..48127740,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1472865	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1532967	0.81[EUR][1000 genomes]
rs17574051	0.87[CEU][hapmap];0.98[GIH][hapmap]
rs2089507	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2940330	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749504	0.81[EUR][1000 genomes]
rs3792623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4694884	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6822209	0.96[CEU][hapmap];0.98[GIH][hapmap];0.84[LWK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs6833403	0.81[EUR][1000 genomes]
rs6854382	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2262771	CNGA1	cis	cerebellum	SCAN
rs2262771	NFXL1	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48106000-48129400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:48114400-48123000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:48116600-48124000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:48118400-48129600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr4:48118600-48128200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:48118800-48127400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:48118800-48128800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:48118800-48129000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:48120600-48126200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:48121600-48124600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr4:48121600-48129400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr4:48121800-48128800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:48122000-48124200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr4:48122200-48123000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr4:48122600-48123000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:48122600-48129400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr4:48122800-48123000	Enhancers	Gastric	stomach
18	chr4:48122800-48123200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:48122800-48123400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:48122800-48124200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr4:48122800-48124800	Enhancers	Primary T cells from cord blood	blood
22	chr4:48122800-48125600	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr4:48122800-48129400	Enhancers	Primary T helper cells fromperipheralblood	blood

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