Variant report

Variant	rs2339043
Chromosome Location	chr15:31125545-31125546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10153041	0.93[CHB][hapmap]
rs10163148	0.84[CHB][hapmap]
rs11070624	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070632	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11070678	0.84[CHB][hapmap]
rs11070718	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs1133642	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs11631543	0.81[ASN][1000 genomes]
rs11631814	0.92[CHB][hapmap]
rs11638295	0.92[CHB][hapmap]
rs11856544	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440244	0.93[CHB][hapmap]
rs12441318	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12441324	0.92[CHB][hapmap]
rs12898883	0.92[CHB][hapmap]
rs12901022	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs12904948	0.92[CHB][hapmap]
rs12904967	0.91[CHB][hapmap]
rs12905321	0.92[CHB][hapmap]
rs12908189	0.93[CHB][hapmap]
rs12911057	0.92[CHB][hapmap]
rs1404468	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs1404469	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs1474381	0.84[CHB][hapmap]
rs1474382	0.84[CHB][hapmap]
rs1524876	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs1524878	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1809483	0.93[CHB][hapmap]
rs1852034	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1880499	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs1880500	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2042613	0.92[CHB][hapmap]
rs2046362	0.92[CHB][hapmap]
rs2113945	0.84[CHB][hapmap]
rs2113946	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2128873	0.93[CHB][hapmap]
rs2177669	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2272218	0.84[CHB][hapmap]
rs2272219	0.84[CHB][hapmap]
rs2293314	0.92[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2293319	0.84[CHB][hapmap]
rs2293320	0.84[CHB][hapmap]
rs2338276	0.93[CHB][hapmap]
rs28376488	0.82[ASN][1000 genomes]
rs28396629	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28453125	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28548813	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28693590	0.84[CHB][hapmap]
rs28708881	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28721380	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2873	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs28795529	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2949566	0.81[ASN][1000 genomes]
rs2949569	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2949570	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs2949573	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2949575	0.84[CHB][hapmap]
rs2949576	0.84[CHB][hapmap]
rs2949577	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs2949578	0.84[CHB][hapmap]
rs2955783	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs2955787	0.84[CHB][hapmap]
rs2955790	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2955791	0.84[CHB][hapmap]
rs2955796	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2955798	0.81[ASN][1000 genomes]
rs2959039	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2959049	0.84[CHB][hapmap]
rs35528291	0.92[CHB][hapmap]
rs3743231	0.84[CHB][hapmap]
rs3829484	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3883068	0.92[CHB][hapmap]
rs4779764	0.92[CHB][hapmap]
rs4779796	0.84[CHB][hapmap]
rs4779797	0.84[CHB][hapmap]
rs56325201	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58844471	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493220	0.92[CHB][hapmap]
rs7161812	0.83[CHB][hapmap]
rs7165798	0.92[CHB][hapmap]
rs7166432	0.93[CHB][hapmap]
rs7169064	0.84[CHB][hapmap]
rs7170710	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs7175951	0.84[CHB][hapmap]
rs7176351	0.84[CHB][hapmap]
rs7178375	0.84[CHB][hapmap]
rs7178533	0.84[CHB][hapmap]
rs7182143	0.92[CHB][hapmap]
rs739831	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7402306	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757341	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798088	0.92[CHB][hapmap]
rs798101	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8023264	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8026481	0.92[CHB][hapmap]
rs8027951	0.92[CHB][hapmap]
rs8040989	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs8041248	0.92[CHB][hapmap]
rs8041717	0.84[CHB][hapmap]
rs8042031	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs811768	0.93[CHB][hapmap]
rs964925	0.88[JPT][hapmap]
rs9806159	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758374	chr15:30292944-31152491	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	esv2760022	chr15:30292944-31177476	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
3	nsv903757	chr15:30369153-31179534	Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv427955	chr15:30467980-31273174	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv1052897	chr15:30501813-31184303	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
6	esv2757593	chr15:30605836-31177476	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv903822	chr15:30899133-31165955	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv533434	chr15:30938215-31244225	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv832950	chr15:30954625-31146464	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1044683	chr15:30954725-31183908	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv542300	chr15:30954725-31183908	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv529701	chr15:30954726-31183907	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
17	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
18	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
19	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
20	nsv903833	chr15:31088443-31174687	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv984044	chr15:31114428-31126547	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2339043	RP11-540B6.2	cis	Whole Blood	GTEx
rs2339043	RP11-540B6.3	cis	lung	GTEx
rs2339043	RP11-540B6.2	cis	lung	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31116200-31125800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:31116200-31126200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:31116200-31126600	Weak transcription	Brain Anterior Caudate	brain
4	chr15:31116200-31128000	Weak transcription	Fetal Brain Female	brain
5	chr15:31116200-31129800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:31116200-31131000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr15:31116200-31133600	Weak transcription	Osteobl	bone
8	chr15:31116200-31134200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:31116200-31135400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:31116200-31135400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:31116200-31136600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:31116400-31126600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:31116400-31130600	Weak transcription	Placenta	Placenta
14	chr15:31116400-31135000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:31117400-31128800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:31120400-31128200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:31120400-31134400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:31120400-31140400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:31121000-31127000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:31121000-31130000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:31121200-31137800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:31122800-31132800	Strong transcription	Dnd41	blood
23	chr15:31123200-31135000	Weak transcription	Primary B cells from cord blood	blood
24	chr15:31124600-31127400	Strong transcription	Spleen	Spleen
25	chr15:31124600-31127800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:31124800-31127400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr15:31124800-31130200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:31125000-31126400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:31125000-31126400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr15:31125000-31126600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr15:31125000-31126800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr15:31125000-31127000	Enhancers	Primary T cells from cord blood	blood
33	chr15:31125000-31127000	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr15:31125000-31127000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:31125000-31127200	Strong transcription	Pancreas	Pancrea
36	chr15:31125000-31127600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr15:31125200-31125600	Strong transcription	Gastric	stomach
38	chr15:31125200-31126200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr15:31125200-31126200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:31125200-31126200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:31125200-31126200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:31125200-31126200	Enhancers	NHEK	skin
43	chr15:31125200-31127000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:31125200-31127000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:31125200-31127200	Enhancers	Primary T cells fromperipheralblood	blood
46	chr15:31125200-31130000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr15:31125400-31125800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:31125400-31126200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr15:31125400-31126200	Enhancers	HMEC	breast
50	chr15:31125400-31126400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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