Variant report

Variant	rs930745
Chromosome Location	chr2:208859893-208859894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10497895	0.81[GIH][hapmap]
rs12464255	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs12465292	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12471242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13431014	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1452521	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17459574	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17459758	0.93[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17537670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17538061	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs28463196	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4502388	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62190863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62190896	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62190898	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62190900	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62190904	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62190905	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62192772	0.82[AMR][1000 genomes]
rs6435402	0.93[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6740362	0.93[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72969822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7565251	0.84[CEU][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7588162	0.87[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs930745	SNORA41	cis	cerebellum	SCAN
rs930745	CREB1	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208834000-208864000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:208834800-208865000	Weak transcription	HSMMtube	muscle
3	chr2:208835800-208860800	Weak transcription	Small Intestine	intestine
4	chr2:208836000-208878400	Weak transcription	Fetal Kidney	kidney
5	chr2:208840000-208863800	Weak transcription	Placenta	Placenta
6	chr2:208841600-208864800	Weak transcription	HepG2	liver
7	chr2:208841600-208865200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr2:208841800-208864800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:208842000-208862000	Weak transcription	Fetal Muscle Leg	muscle
10	chr2:208842000-208864200	Weak transcription	Fetal Thymus	thymus
11	chr2:208842200-208861800	Weak transcription	Adipose Nuclei	Adipose
12	chr2:208842200-208861800	Weak transcription	Liver	Liver
13	chr2:208842200-208862000	Weak transcription	Lung	lung
14	chr2:208842200-208862400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:208842200-208862400	Weak transcription	Left Ventricle	heart
16	chr2:208842200-208862400	Weak transcription	Ovary	ovary
17	chr2:208842200-208864200	Weak transcription	Fetal Brain Female	brain
18	chr2:208842200-208864200	Weak transcription	Fetal Lung	lung
19	chr2:208842200-208864400	Weak transcription	Brain Substantia Nigra	brain
20	chr2:208842200-208864400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:208842200-208864600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr2:208842200-208864800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:208842200-208864800	Weak transcription	Aorta	Aorta
24	chr2:208842200-208864800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:208842200-208864800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:208842200-208864800	Weak transcription	Right Ventricle	heart
27	chr2:208842200-208865000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:208842200-208866600	Weak transcription	Gastric	stomach
29	chr2:208842200-208867600	Weak transcription	Thymus	Thymus
30	chr2:208842200-208871200	Weak transcription	Esophagus	oesophagus
31	chr2:208842400-208861000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr2:208842400-208864200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:208842400-208864400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:208842400-208864800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:208842400-208866000	Weak transcription	Brain Germinal Matrix	brain
36	chr2:208842400-208867200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr2:208842400-208868200	Weak transcription	Dnd41	blood
38	chr2:208842600-208864000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:208842800-208862400	Weak transcription	Fetal Stomach	stomach
40	chr2:208843400-208861800	Weak transcription	Right Atrium	heart
41	chr2:208843600-208871200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:208848800-208862600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:208848800-208864000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:208848800-208864200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:208848800-208864800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:208849000-208861200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:208852200-208864800	Weak transcription	Spleen	Spleen
48	chr2:208852400-208864800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr2:208852400-208867200	Weak transcription	Psoas Muscle	Psoas
50	chr2:208852400-208868000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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