Variant report

Variant	rs7939724
Chromosome Location	chr11:9545849-9545850
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr11:9545670-9546412	SK-N-SH	brain:	n/a	chr11:9546167-9546176
2	NFIC	chr11:9545707-9546373	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9545230..9547236-chr11:10828950..10831720,2	K562	blood:

Variant related genes	Relation type
ZNF143	TF binding region
ENSG00000110321	Chromatin interaction
ENSG00000246308	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1020621	0.85[CEU][hapmap]
rs10770037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840243	0.89[CEU][hapmap];0.87[CHD][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap]
rs10840245	0.90[CHD][hapmap];0.83[MEX][hapmap]
rs10840249	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042350	0.80[CEU][hapmap];0.87[MEX][hapmap]
rs11042366	0.85[CEU][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1470895	0.82[EUR][1000 genomes]
rs1470896	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2278900	0.90[CHD][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap]
rs2290423	0.85[CEU][hapmap];0.88[MEX][hapmap]
rs2290424	0.92[ASW][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs2290425	0.90[CHD][hapmap];0.83[MEX][hapmap]
rs3763873	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs3763874	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]
rs3763877	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41369549	0.83[MEX][hapmap]
rs4810	0.83[MEX][hapmap]
rs4910048	0.81[CEU][hapmap]
rs4910468	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6486394	0.90[CHD][hapmap]
rs7104568	0.83[MEX][hapmap]
rs7122252	0.85[CEU][hapmap];0.88[MEX][hapmap]
rs723297	0.90[CHD][hapmap]
rs727405	0.85[CEU][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs729313	0.90[CHD][hapmap]
rs7926589	0.89[CEU][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7927350	0.84[CEU][hapmap];0.88[MEX][hapmap]
rs7938998	0.89[AFR][1000 genomes]
rs7944578	0.85[CEU][hapmap];0.88[MEX][hapmap]
rs8785	0.84[CEU][hapmap];0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7939724	IPO7	Cis_1M	lymphoblastoid	RTeQTL
rs7939724	SNORA23	cis	parietal	SCAN
rs7939724	SNORA23	cis	cerebellum	SCAN

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	chr11:9532600-9546400	Weak transcription	Stomach Mucosa	stomach
9	chr11:9533400-9550600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr11:9534600-9546800	Weak transcription	Gastric	stomach
11	chr11:9534600-9556800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:9535000-9548400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:9535000-9548800	Weak transcription	NHEK	skin
14	chr11:9535200-9548800	Weak transcription	Fetal Brain Male	brain
15	chr11:9535200-9551200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr11:9535400-9550800	Weak transcription	Brain Anterior Caudate	brain
17	chr11:9535800-9548600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:9535800-9549000	Weak transcription	Aorta	Aorta
19	chr11:9535800-9550800	Weak transcription	Esophagus	oesophagus
20	chr11:9535800-9554800	Weak transcription	Ovary	ovary
21	chr11:9536200-9550600	Weak transcription	HSMMtube	muscle
22	chr11:9536200-9552400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:9536400-9554800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:9537400-9551200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr11:9538000-9546800	Weak transcription	Lung	lung
26	chr11:9538000-9550800	Weak transcription	Right Ventricle	heart
27	chr11:9538200-9546800	Weak transcription	Brain Hippocampus Middle	brain
28	chr11:9538200-9547400	Weak transcription	Spleen	Spleen
29	chr11:9538200-9548600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr11:9538200-9548600	Weak transcription	Hela-S3	cervix
31	chr11:9538200-9549000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr11:9538200-9550400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr11:9538200-9550800	Weak transcription	Brain Substantia Nigra	brain
34	chr11:9538400-9548600	Weak transcription	A549	lung
35	chr11:9538400-9548800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr11:9538600-9546800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:9538600-9547000	Weak transcription	Psoas Muscle	Psoas
38	chr11:9538600-9548200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:9538600-9548800	Weak transcription	Brain Angular Gyrus	brain
40	chr11:9538800-9546400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr11:9538800-9546400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:9538800-9548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:9538800-9562000	Weak transcription	Small Intestine	intestine
44	chr11:9539000-9546400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:9539000-9546400	Weak transcription	Colon Smooth Muscle	Colon
46	chr11:9539000-9550800	Weak transcription	Brain Germinal Matrix	brain
47	chr11:9539200-9546400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:9539200-9546400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr11:9539200-9546600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:9539200-9546800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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