Variant report

Variant	rs7940441
Chromosome Location	chr11:46939027-46939028
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:46933810..46936759-chr11:46937673..46939969,2	MCF-7	breast:
2	chr11:46936734..46939030-chr11:46940693..46942577,2	K562	blood:
3	chr11:46938691..46940925-chr17:56734920..56736797,2	MCF-7	breast:
4	chr11:46933026..46934959-chr11:46937593..46939848,2	K562	blood:

Variant related genes	Relation type
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1007738	0.92[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs10734548	0.89[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs10734549	0.82[EUR][1000 genomes]
rs10742784	0.87[EUR][1000 genomes]
rs10769208	0.82[EUR][1000 genomes]
rs10769211	0.92[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs10769212	0.87[EUR][1000 genomes]
rs10769225	0.84[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10769226	0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10769227	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10769228	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10769234	0.82[CHB][hapmap]
rs10838620	0.81[EUR][1000 genomes]
rs10838629	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10838635	0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10838640	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10838641	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10838644	0.86[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap]
rs10838646	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs10838652	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap]
rs10838658	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11039002	0.82[JPT][hapmap]
rs11039014	0.92[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs11039028	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039033	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039035	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11039074	0.80[CHB][hapmap]
rs11039097	0.83[GIH][hapmap]
rs11600292	0.86[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11602250	0.84[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11606992	0.90[ASN][1000 genomes]
rs11608083	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12417519	0.80[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs12796744	0.86[GIH][hapmap]
rs12807111	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1551744	0.92[GIH][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs17790204	0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2035068	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2070852	0.81[GIH][hapmap];0.96[MEX][hapmap]
rs2290884	0.87[EUR][1000 genomes]
rs2306026	0.87[EUR][1000 genomes]
rs2306027	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2306028	0.82[JPT][hapmap]
rs2306033	0.82[JPT][hapmap]
rs2306035	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2306036	0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap]
rs2306037	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2903522	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3136441	0.82[JPT][hapmap]
rs3136447	0.82[JPT][hapmap]
rs3136457	0.80[JPT][hapmap]
rs3136460	0.82[JPT][hapmap]
rs34340483	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3816614	0.87[EUR][1000 genomes]
rs3829940	0.84[EUR][1000 genomes]
rs4076557	0.82[JPT][hapmap]
rs4294527	0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs4394802	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4494268	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs4528282	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs4548577	0.80[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4581406	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4587689	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap]
rs4752815	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4752816	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4752932	0.82[JPT][hapmap]
rs4752933	0.82[JPT][hapmap]
rs4752946	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs4752947	0.82[JPT][hapmap]
rs4752951	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4752957	0.86[GIH][hapmap]
rs5896	0.82[JPT][hapmap]
rs6485695	0.82[EUR][1000 genomes]
rs6485696	0.86[GIH][hapmap];0.84[MEX][hapmap]
rs6485702	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs6485715	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6485716	0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs6485726	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap]
rs7101374	0.92[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs7103581	0.86[GIH][hapmap]
rs7107778	0.89[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs7108822	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs7108902	0.86[GIH][hapmap]
rs7109707	0.82[EUR][1000 genomes]
rs7111270	0.81[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7112854	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap]
rs7118170	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7123632	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7124648	0.80[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs7125807	0.86[GIH][hapmap]
rs7126005	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs7128193	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7128650	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs7130947	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7480140	0.82[EUR][1000 genomes]
rs7929294	0.83[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap]
rs7929688	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7931260	0.86[GIH][hapmap]
rs7934421	0.82[EUR][1000 genomes]
rs7935346	0.95[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7938169	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7939786	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7941252	0.86[EUR][1000 genomes]
rs7943866	0.84[EUR][1000 genomes]
rs7945315	0.86[GIH][hapmap]
rs7945558	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7946709	0.86[GIH][hapmap]
rs7946739	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7950753	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap]
rs964551	0.89[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][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	esv3354576	chr11:46938801-46941349	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7940441	ACP2	cis	lymphoblastoid	seeQTL
rs7940441	NUP160	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46937600-46939800	Active TSS	Fetal Kidney	kidney
2	chr11:46937800-46939200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr11:46937800-46939400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr11:46937800-46939400	Flanking Active TSS	HMEC	breast
5	chr11:46937800-46939800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:46937800-46940400	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr11:46937800-46940400	Active TSS	Brain Anterior Caudate	brain
8	chr11:46937800-46940400	Active TSS	Brain Cingulate Gyrus	brain
9	chr11:46937800-46940400	Active TSS	HSMMtube	muscle
10	chr11:46938000-46939200	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr11:46938000-46939200	Flanking Active TSS	Rectal Smooth Muscle	rectum
12	chr11:46938000-46939200	Active TSS	Right Atrium	heart
13	chr11:46938000-46939400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
14	chr11:46938000-46939400	Flanking Active TSS	NHEK	skin
15	chr11:46938000-46939600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:46938000-46939600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:46938000-46939600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr11:46938000-46939600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:46938000-46939600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
20	chr11:46938000-46939600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
21	chr11:46938000-46939600	Flanking Active TSS	Placenta	Placenta
22	chr11:46938000-46939600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr11:46938000-46939600	Flanking Active TSS	Osteobl	bone
24	chr11:46938000-46939800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
25	chr11:46938000-46940400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:46938000-46940600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:46938000-46940600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:46938000-46940600	Active TSS	Ovary	ovary
29	chr11:46938000-46940600	Flanking Bivalent TSS/Enh	Thymus	Thymus
30	chr11:46938000-46940800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr11:46938000-46940800	Active TSS	H9 Cell Line	embryonic stem cell
32	chr11:46938000-46941200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:46938200-46939200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:46938200-46939200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
35	chr11:46938200-46939200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
36	chr11:46938200-46939400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
37	chr11:46938200-46939400	Flanking Active TSS	Liver	Liver
38	chr11:46938200-46939600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr11:46938200-46939600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr11:46938200-46939600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
41	chr11:46938200-46939600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
42	chr11:46938200-46939600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
43	chr11:46938200-46939600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
44	chr11:46938200-46939800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
45	chr11:46938200-46939800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
46	chr11:46938200-46939800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:46938200-46939800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
48	chr11:46938200-46939800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
49	chr11:46938200-46940400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
50	chr11:46938200-46940400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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