Variant report

Variant	rs10032941
Chromosome Location	chr4:15402115-15402116
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	chr4:15401621..15404342-chr4:15426041..15427712,2	MCF-7	breast:
2	chr4:15396902..15399752-chr4:15401577..15403886,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10002931	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10003338	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212844	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10212901	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213628	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024758	0.81[CEU][hapmap]
rs1048037	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10488970	0.82[EUR][1000 genomes]
rs11934015	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11937671	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233742	0.83[EUR][1000 genomes]
rs13106702	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13114788	0.83[EUR][1000 genomes]
rs13123785	0.80[CEU][hapmap]
rs13124324	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124984	0.82[EUR][1000 genomes]
rs13131227	0.86[CHD][hapmap]
rs13132007	0.83[EUR][1000 genomes]
rs13132446	0.83[EUR][1000 genomes]
rs13132604	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs13138481	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs16891929	0.80[EUR][1000 genomes]
rs16891934	0.80[EUR][1000 genomes]
rs1990524	0.82[EUR][1000 genomes]
rs2160043	0.84[JPT][hapmap]
rs2160046	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2192355	0.82[EUR][1000 genomes]
rs2192363	0.85[ASN][1000 genomes]
rs2192364	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215810	0.85[ASN][1000 genomes]
rs28376639	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2872704	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34028526	0.83[EUR][1000 genomes]
rs34351987	0.83[EUR][1000 genomes]
rs34352292	0.83[EUR][1000 genomes]
rs35866305	0.83[EUR][1000 genomes]
rs35971217	0.83[EUR][1000 genomes]
rs3797006	0.81[CEU][hapmap]
rs3822296	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140932	0.86[ASN][1000 genomes]
rs59684117	0.83[EUR][1000 genomes]
rs61240629	0.83[EUR][1000 genomes]
rs62289285	0.83[EUR][1000 genomes]
rs6449138	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855244	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71601473	0.82[EUR][1000 genomes]
rs7442554	0.82[EUR][1000 genomes]
rs7661287	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7681816	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7687272	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690471	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697778	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973629	0.85[ASN][1000 genomes]
rs9991652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10032941	SLC39A8	trans	cerebellum	SCAN
rs10032941	HS3ST1	cis	parietal	SCAN
rs10032941	CPEB2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15394400-15402400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:15397000-15402200	Weak transcription	Right Atrium	heart
3	chr4:15398000-15402200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:15399000-15402200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:15399000-15402400	Enhancers	Hela-S3	cervix
6	chr4:15399000-15405200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr4:15399200-15402400	Enhancers	NHEK	skin
8	chr4:15399600-15402200	Enhancers	Stomach Smooth Muscle	stomach
9	chr4:15400000-15402400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:15400000-15402400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:15400000-15402800	Enhancers	Colon Smooth Muscle	Colon
12	chr4:15400000-15405400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr4:15400200-15402200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr4:15400200-15402800	Enhancers	Primary T cells from cord blood	blood
15	chr4:15400200-15403200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:15400200-15403200	Enhancers	Ovary	ovary
17	chr4:15400200-15403400	Enhancers	Primary B cells from peripheral blood	blood
18	chr4:15400200-15405000	Enhancers	Primary hematopoietic stem cells	blood
19	chr4:15400400-15402200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:15400400-15402600	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr4:15400400-15403600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr4:15400600-15402400	Weak transcription	Lung	lung
23	chr4:15400600-15403600	Enhancers	Fetal Kidney	kidney
24	chr4:15400800-15402200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:15400800-15402400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:15400800-15402400	Weak transcription	Spleen	Spleen
27	chr4:15401000-15402200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr4:15401000-15402200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:15401000-15402200	Weak transcription	Esophagus	oesophagus
30	chr4:15401200-15402400	Enhancers	Primary B cells from cord blood	blood
31	chr4:15401200-15405400	Enhancers	Rectal Smooth Muscle	rectum
32	chr4:15401400-15402200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:15401400-15402200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:15401400-15402800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:15401400-15402800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:15401400-15405200	Enhancers	NHLF	lung
37	chr4:15401600-15402200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:15401600-15402400	Enhancers	Osteobl	bone
39	chr4:15401600-15402600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr4:15401600-15403000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr4:15401600-15404000	Enhancers	HMEC	breast
42	chr4:15401600-15404200	Enhancers	HSMM	muscle
43	chr4:15401600-15405000	Enhancers	HSMMtube	muscle
44	chr4:15401600-15405200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:15401800-15402400	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr4:15401800-15402600	Enhancers	Adipose Nuclei	Adipose
47	chr4:15401800-15403200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:15401800-15403200	Enhancers	Placenta	Placenta
49	chr4:15401800-15404000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:15401800-15404000	Enhancers	Fetal Stomach	stomach

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