Variant report

Variant	rs2638041
Chromosome Location	chr3:112248774-112248775
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10934177	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1385527	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386896	1.00[ASN][1000 genomes]
rs1388442	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472106	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472107	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488260	1.00[ASN][1000 genomes]
rs1488262	1.00[ASN][1000 genomes]
rs1491629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532198	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552707	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814053	1.00[ASN][1000 genomes]
rs1817694	1.00[ASN][1000 genomes]
rs1844864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877362	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877364	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1906519	1.00[ASN][1000 genomes]
rs2029317	1.00[ASN][1000 genomes]
rs2399431	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464612	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638025	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638030	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638033	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638036	1.00[ASN][1000 genomes]
rs2638043	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2638044	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668216	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2705510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705514	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705520	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705524	1.00[ASN][1000 genomes]
rs2705551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705554	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705563	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933140	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2969894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109033	0.86[ASN][1000 genomes]
rs62264580	0.83[ASN][1000 genomes]
rs6793232	1.00[ASN][1000 genomes]
rs7618978	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901829	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs971832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv965197	chr3:112238965-112250194	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112227400-112269800	Weak transcription	Small Intestine	intestine
2	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:112237200-112254200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:112238600-112249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:112241000-112251600	Weak transcription	HUVEC	blood vessel
7	chr3:112241600-112259400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:112242200-112252200	Weak transcription	NHLF	lung
9	chr3:112242400-112249800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:112242600-112263800	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:112243000-112271600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:112244000-112259800	Weak transcription	Pancreas	Pancrea
13	chr3:112244200-112251200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:112244400-112274200	Weak transcription	Stomach Mucosa	stomach
15	chr3:112244400-112278200	Weak transcription	K562	blood
16	chr3:112244400-112278400	Weak transcription	HSMMtube	muscle
17	chr3:112244600-112256200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:112244600-112264800	Weak transcription	NHEK	skin
19	chr3:112245000-112249600	Strong transcription	Liver	Liver
20	chr3:112245000-112249800	Strong transcription	Adipose Nuclei	Adipose
21	chr3:112245200-112263200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:112245200-112273200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:112245400-112262800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:112245600-112249600	Strong transcription	Brain Hippocampus Middle	brain
25	chr3:112245600-112249800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr3:112245600-112249800	Strong transcription	Placenta	Placenta
27	chr3:112245600-112250000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:112245600-112250000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:112245600-112250800	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:112245600-112252000	Weak transcription	Fetal Kidney	kidney
31	chr3:112245600-112258000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr3:112245600-112258200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:112245800-112249000	Strong transcription	Primary T cells from cord blood	blood
34	chr3:112245800-112249200	Strong transcription	Psoas Muscle	Psoas
35	chr3:112245800-112249400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:112245800-112249400	Strong transcription	Thymus	Thymus
37	chr3:112245800-112249600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:112245800-112249800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr3:112245800-112249800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:112245800-112249800	Strong transcription	Fetal Intestine Large	intestine
41	chr3:112245800-112249800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:112245800-112250000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:112245800-112252000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:112245800-112252600	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:112245800-112257400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:112245800-112261400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:112245800-112261800	Strong transcription	Dnd41	blood
48	chr3:112245800-112279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:112246000-112248800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:112246000-112249400	Weak transcription	Hela-S3	cervix

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