Variant report

Variant	rs3763874
Chromosome Location	chr11:9546587-9546588
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	chr11:9545230..9547236-chr11:10828950..10831720,2	K562	blood:
2	chr11:9481080..9484532-chr11:9545856..9548015,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110321	Chromatin interaction
ENSG00000268403	Chromatin interaction
ENSG00000166478	Chromatin interaction
ENSG00000246308	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10770034	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10770037	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs10840243	0.87[CHD][hapmap];0.80[MEX][hapmap]
rs10840245	0.89[CEU][hapmap];0.90[CHD][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs10840253	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs11042377	0.80[AMR][1000 genomes]
rs11042393	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042395	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11042397	0.85[EUR][1000 genomes]
rs11601316	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12792161	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12806418	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17258462	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2278900	0.89[CEU][hapmap];0.90[CHD][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2290424	0.92[ASW][hapmap];0.85[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2290425	0.85[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41369549	0.81[CEU][hapmap];0.92[MEX][hapmap]
rs4810	0.81[CEU][hapmap];0.96[MEX][hapmap]
rs4910053	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6486394	0.90[CHD][hapmap]
rs7104568	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs723297	0.90[CHD][hapmap]
rs727405	0.90[CHD][hapmap]
rs729313	0.90[CHD][hapmap]
rs7926589	0.87[CHD][hapmap];0.80[MEX][hapmap]
rs7938998	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7939724	1.00[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8785	0.80[MEX][hapmap]
rs972594	0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3763874	SNORA23	cis	cerebellum	SCAN
rs3763874	IPO7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9491400-9551600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr11:9523400-9550800	Weak transcription	Colonic Mucosa	Colon
3	chr11:9523400-9551000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:9528800-9550400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:9529200-9550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:9530200-9551000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr11:9531000-9550800	Weak transcription	Pancreas	Pancrea
8	chr11:9533400-9550600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr11:9534600-9546800	Weak transcription	Gastric	stomach
10	chr11:9534600-9556800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:9535000-9548400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:9535000-9548800	Weak transcription	NHEK	skin
13	chr11:9535200-9548800	Weak transcription	Fetal Brain Male	brain
14	chr11:9535200-9551200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr11:9535400-9550800	Weak transcription	Brain Anterior Caudate	brain
16	chr11:9535800-9548600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:9535800-9549000	Weak transcription	Aorta	Aorta
18	chr11:9535800-9550800	Weak transcription	Esophagus	oesophagus
19	chr11:9535800-9554800	Weak transcription	Ovary	ovary
20	chr11:9536200-9550600	Weak transcription	HSMMtube	muscle
21	chr11:9536200-9552400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:9536400-9554800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr11:9537400-9551200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr11:9538000-9546800	Weak transcription	Lung	lung
25	chr11:9538000-9550800	Weak transcription	Right Ventricle	heart
26	chr11:9538200-9546800	Weak transcription	Brain Hippocampus Middle	brain
27	chr11:9538200-9547400	Weak transcription	Spleen	Spleen
28	chr11:9538200-9548600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr11:9538200-9548600	Weak transcription	Hela-S3	cervix
30	chr11:9538200-9549000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr11:9538200-9550400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr11:9538200-9550800	Weak transcription	Brain Substantia Nigra	brain
33	chr11:9538400-9548600	Weak transcription	A549	lung
34	chr11:9538400-9548800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr11:9538600-9546800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:9538600-9547000	Weak transcription	Psoas Muscle	Psoas
37	chr11:9538600-9548200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr11:9538600-9548800	Weak transcription	Brain Angular Gyrus	brain
39	chr11:9538800-9548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:9538800-9562000	Weak transcription	Small Intestine	intestine
41	chr11:9539000-9550800	Weak transcription	Brain Germinal Matrix	brain
42	chr11:9539200-9546600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:9539200-9546800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:9539200-9546800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:9539200-9546800	Weak transcription	Left Ventricle	heart
46	chr11:9539200-9548600	Weak transcription	NHLF	lung
47	chr11:9539200-9549000	Weak transcription	HMEC	breast
48	chr11:9539400-9548600	Weak transcription	Fetal Intestine Large	intestine
49	chr11:9539600-9546800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr11:9539600-9548000	Weak transcription	HUVEC	blood vessel

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