Variant report

Variant	rs1029890
Chromosome Location	chr2:235126491-235126492
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1013546	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10178233	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12617671	0.81[EUR][1000 genomes]
rs12618611	0.81[EUR][1000 genomes]
rs1507520	0.80[EUR][1000 genomes]
rs1860699	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7421360	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers 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	37 gene(s)	inside rSNPs	diseases
3	nsv584713	chr2:235092011-235236611	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1029890	SNORA75	cis	cerebellum	SCAN
rs1029890	GPR55	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:235121800-235126800	Weak transcription	Adipose Nuclei	Adipose
2	chr2:235123400-235128800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr2:235123600-235128200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:235123600-235128200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr2:235123800-235128200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:235124000-235127200	Weak transcription	Spleen	Spleen
7	chr2:235124000-235128000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr2:235124000-235128400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:235124400-235128800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr2:235124600-235127600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:235124600-235129000	Enhancers	Dnd41	blood
12	chr2:235124800-235127600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr2:235124800-235128000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:235124800-235128000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr2:235125600-235127600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr2:235125600-235127600	Enhancers	NHEK	skin
17	chr2:235125800-235126600	Enhancers	Esophagus	oesophagus
18	chr2:235125800-235127200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:235125800-235127600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:235125800-235127800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:235125800-235128400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:235125800-235128400	Enhancers	Primary T cells from cord blood	blood
23	chr2:235126000-235126600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr2:235126000-235127000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:235126200-235127200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:235126200-235127400	Enhancers	HMEC	breast

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