Variant report

Variant	rs10840441
Chromosome Location	chr11:10593006-10593007
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	chr11:10561599..10564303-chr11:10591850..10593448,2	K562	blood:
2	chr11:10569352..10571192-chr11:10591337..10594037,2	K562	blood:

Variant related genes	Relation type
ENSG00000110315	Chromatin interaction
ENSG00000177112	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10219205	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10219352	0.87[ASN][1000 genomes]
rs1062912	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10770123	0.82[TSI][hapmap]
rs10770126	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs10840438	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840440	0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10840443	0.90[JPT][hapmap]
rs10840444	0.84[ASN][1000 genomes]
rs10840446	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10840448	0.81[ASN][1000 genomes]
rs11042875	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11042876	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11042877	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11042879	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042882	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11042883	0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11042894	0.86[ASN][1000 genomes]
rs11042895	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs11042897	0.81[ASN][1000 genomes]
rs11042898	0.84[ASN][1000 genomes]
rs11827503	0.84[ASN][1000 genomes]
rs12288969	0.97[ASN][1000 genomes]
rs12576545	0.84[ASN][1000 genomes]
rs12576547	0.81[ASN][1000 genomes]
rs16907989	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1964537	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1993818	0.82[TSI][hapmap]
rs1993819	0.82[TSI][hapmap]
rs2241489	0.82[ASN][1000 genomes]
rs2278125	0.80[CHB][hapmap];0.82[MEX][hapmap]
rs2288236	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs34988160	0.81[ASN][1000 genomes]
rs3741033	0.90[JPT][hapmap]
rs3741034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3741042	0.85[ASN][1000 genomes]
rs4910153	0.82[TSI][hapmap]
rs4910162	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7114453	0.83[ASN][1000 genomes]
rs7114603	0.85[ASN][1000 genomes]
rs7115310	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7115735	0.81[ASN][1000 genomes]
rs7118551	0.88[ASN][1000 genomes]
rs7126245	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs724723	0.83[ASN][1000 genomes]
rs7358373	0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs746164	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs749045	0.82[ASN][1000 genomes]
rs7941294	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs918981	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs964425	0.81[ASN][1000 genomes]
rs964426	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10840441	MRVI1	cis	multi-tissue	Pritchard
rs10840441	RNF141	cis	parietal	SCAN
rs10840441	AMPD3	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10573000-10603200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:10580600-10609800	Weak transcription	Thymus	Thymus
3	chr11:10583000-10600000	Weak transcription	Fetal Intestine Large	intestine
4	chr11:10583200-10601800	Weak transcription	Fetal Intestine Small	intestine
5	chr11:10583600-10595800	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:10586200-10594400	Weak transcription	Fetal Stomach	stomach
7	chr11:10586200-10594800	Weak transcription	Spleen	Spleen
8	chr11:10586400-10620400	Weak transcription	Brain Anterior Caudate	brain
9	chr11:10586600-10594000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:10587200-10594200	Weak transcription	Primary B cells from cord blood	blood
11	chr11:10587200-10594400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr11:10587200-10595600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:10587600-10605000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr11:10588200-10594400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:10588400-10595800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr11:10588600-10602800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:10589000-10594000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:10589000-10595000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:10590200-10594400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:10590200-10595000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr11:10590200-10595000	Weak transcription	Placenta	Placenta
22	chr11:10590200-10597000	Weak transcription	Fetal Lung	lung
23	chr11:10590200-10597600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr11:10590400-10597000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:10590600-10594000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:10590600-10594800	Weak transcription	Lung	lung
27	chr11:10590600-10594800	Weak transcription	Right Ventricle	heart
28	chr11:10590600-10594800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr11:10590600-10595200	Weak transcription	Brain Hippocampus Middle	brain
30	chr11:10590600-10595600	Weak transcription	Ovary	ovary
31	chr11:10590600-10600200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr11:10590600-10601600	Weak transcription	Adipose Nuclei	Adipose
33	chr11:10590600-10605600	Weak transcription	NH-A	brain
34	chr11:10590600-10611200	Weak transcription	Pancreas	Pancrea
35	chr11:10590800-10593200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr11:10590800-10608200	Weak transcription	NHDF-Ad	bronchial
37	chr11:10591400-10603200	Weak transcription	Osteobl	bone
38	chr11:10591800-10594400	Weak transcription	HUVEC	blood vessel
39	chr11:10591800-10594600	Weak transcription	Fetal Muscle Leg	muscle
40	chr11:10591800-10597000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr11:10591800-10600400	Weak transcription	Brain Substantia Nigra	brain
42	chr11:10592000-10593600	Weak transcription	Aorta	Aorta
43	chr11:10592000-10594000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:10592000-10594400	Weak transcription	Left Ventricle	heart
45	chr11:10592000-10594600	Weak transcription	Right Atrium	heart
46	chr11:10592000-10594800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr11:10592000-10597000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr11:10592000-10600200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:10592000-10602800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr11:10592000-10608000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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