Variant report

Variant	rs10840253
Chromosome Location	chr11:9553209-9553210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9552590..9554469-chr11:9597460..9599554,2	K562	blood:
2	chr11:9550857..9553368-chr11:9594096..9596609,4	K562	blood:
3	chr11:9483396..9484956-chr11:9552157..9554258,2	MCF-7	breast:
4	chr11:9549975..9559413-chr11:9590114..9600515,26	MCF-7	breast:
5	chr11:9547770..9558262-chr11:9588302..9599721,48	MCF-7	breast:
6	chr11:9549821..9553673-chr11:9553881..9558124,6	K562	blood:

Variant related genes	Relation type
ENSG00000238387	Chromatin interaction
ENSG00000166478	Chromatin interaction
ENSG00000166483	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1020621	0.86[JPT][hapmap]
rs10770028	0.86[JPT][hapmap]
rs10770032	0.86[JPT][hapmap]
rs10770034	0.80[EUR][1000 genomes]
rs10840228	0.86[JPT][hapmap]
rs10840235	0.80[JPT][hapmap]
rs10840243	0.81[JPT][hapmap]
rs10840245	0.85[CEU][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs10840252	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11042328	0.86[JPT][hapmap]
rs11042366	0.86[JPT][hapmap]
rs11042393	0.83[EUR][1000 genomes]
rs11042395	0.81[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs11042397	0.85[EUR][1000 genomes]
rs11601316	0.88[EUR][1000 genomes]
rs12792161	0.81[EUR][1000 genomes]
rs12795344	0.86[JPT][hapmap]
rs12806418	0.81[EUR][1000 genomes]
rs2278900	0.85[CEU][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2290423	0.82[JPT][hapmap]
rs2290424	0.82[CEU][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs2290425	0.82[CEU][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs3763873	0.82[ASN][1000 genomes]
rs3763874	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs41369549	0.86[JPT][hapmap];0.87[MEX][hapmap]
rs4625466	0.82[JPT][hapmap]
rs4810	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs4910053	0.84[CEU][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs6486307	0.86[JPT][hapmap]
rs6486361	0.86[JPT][hapmap]
rs6486394	0.81[JPT][hapmap]
rs7104568	0.81[CEU][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs7122252	0.86[JPT][hapmap]
rs723297	0.81[JPT][hapmap]
rs727405	0.81[JPT][hapmap]
rs729313	0.81[JPT][hapmap]
rs7483667	0.81[EUR][1000 genomes]
rs7926589	0.81[JPT][hapmap]
rs7927350	0.81[JPT][hapmap]
rs7938998	0.86[EUR][1000 genomes]
rs7944578	0.81[JPT][hapmap]
rs8785	0.85[JPT][hapmap]
rs972594	0.81[JPT][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
rs10840253	IPO7	Cis_1M	lymphoblastoid	RTeQTL
rs10840253	SNORA23	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9534600-9556800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:9535800-9554800	Weak transcription	Ovary	ovary
3	chr11:9536400-9554800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:9538800-9562000	Weak transcription	Small Intestine	intestine
5	chr11:9545000-9555000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:9547400-9556400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:9547600-9569800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:9547800-9557000	Weak transcription	Spleen	Spleen
9	chr11:9547800-9586600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:9548200-9554800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr11:9549200-9554200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:9549400-9554000	Weak transcription	Fetal Brain Female	brain
13	chr11:9549400-9555600	Weak transcription	HMEC	breast
14	chr11:9549400-9556200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:9549400-9581000	Weak transcription	Primary B cells from cord blood	blood
16	chr11:9549600-9554000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:9549600-9555000	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:9549800-9554800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:9549800-9578200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr11:9550400-9553600	Enhancers	Placenta	Placenta
21	chr11:9550600-9556400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr11:9550600-9556400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr11:9550600-9586600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:9550800-9554800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:9550800-9554800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:9550800-9554800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:9551000-9554800	Weak transcription	NH-A	brain
28	chr11:9551000-9581200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr11:9551200-9556200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr11:9551200-9556400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr11:9551200-9570600	Weak transcription	Thymus	Thymus
32	chr11:9551400-9554800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:9551400-9554800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:9551400-9554800	Weak transcription	Osteobl	bone
35	chr11:9551400-9555000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:9551400-9556200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:9551400-9556400	Weak transcription	NHDF-Ad	bronchial
38	chr11:9551400-9556800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:9551400-9562600	Weak transcription	Pancreas	Pancrea
40	chr11:9551400-9582600	Weak transcription	Primary T cells from cord blood	blood
41	chr11:9551600-9554800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr11:9551600-9555200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:9551600-9556800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr11:9551600-9556800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:9551800-9554600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr11:9551800-9554800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:9551800-9555000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr11:9551800-9555000	Weak transcription	NHLF	lung
49	chr11:9551800-9556000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:9551800-9556200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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