Variant report

Variant	rs2140733
Chromosome Location	chr15:31134146-31134147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10047979	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10152819	1.00[CHB][hapmap]
rs10162919	1.00[JPT][hapmap]
rs1043251	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10467918	0.94[ASN][1000 genomes]
rs1088471	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1088475	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898290	1.00[JPT][hapmap]
rs12902573	1.00[JPT][hapmap]
rs12903674	0.88[ASN][1000 genomes]
rs12911930	1.00[JPT][hapmap]
rs12913087	1.00[JPT][hapmap]
rs12915504	1.00[JPT][hapmap]
rs13380246	1.00[CHB][hapmap]
rs1524877	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16956469	1.00[CHB][hapmap]
rs16956471	1.00[CHB][hapmap]
rs2204391	0.86[AFR][1000 genomes]
rs2339046	1.00[CHB][hapmap]
rs2691682	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860452	1.00[CHB][hapmap]
rs2955778	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2955781	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2955782	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955788	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2955789	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2955792	1.00[CHB][hapmap]
rs34178381	0.82[ASN][1000 genomes]
rs35619616	0.82[ASN][1000 genomes]
rs3784589	1.00[JPT][hapmap]
rs4779789	0.96[AMR][1000 genomes]
rs4779792	0.94[ASN][1000 genomes]
rs4779793	0.84[ASN][1000 genomes]
rs565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6493352	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs711223	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71473153	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71474639	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7161796	1.00[JPT][hapmap]
rs7167074	1.00[JPT][hapmap]
rs7171212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7182547	1.00[JPT][hapmap]
rs798081	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798083	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798085	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798087	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798100	0.81[AMR][1000 genomes]
rs798104	0.94[GIH][hapmap];0.92[TSI][hapmap]
rs798118	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798119	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs798120	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798121	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798122	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798123	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798124	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798126	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798128	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798129	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798130	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs798131	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8023754	0.88[ASN][1000 genomes]
rs8026711	0.94[ASN][1000 genomes]
rs8029960	0.88[ASN][1000 genomes]
rs8036676	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs811304	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv832951	chr15:31131239-31304469	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2140733	FAN1	cis	Whole Blood	GTEx
rs2140733	FAN1	cis	lymphoblastoid	seeQTL
rs2140733	MTMR15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31116200-31134200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr15:31116200-31135400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:31116200-31135400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:31116200-31136600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:31116400-31135000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr15:31120400-31134400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:31120400-31140400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:31121200-31137800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:31123200-31135000	Weak transcription	Primary B cells from cord blood	blood
10	chr15:31125600-31140400	Weak transcription	Gastric	stomach
11	chr15:31126200-31134200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr15:31127000-31157800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:31127200-31170000	Weak transcription	Pancreas	Pancrea
14	chr15:31127600-31135400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr15:31127800-31137800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:31132800-31134400	Weak transcription	Dnd41	blood
17	chr15:31132800-31137800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:31132800-31195600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:31133200-31136800	Enhancers	Primary T cells from cord blood	blood
20	chr15:31133600-31136400	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr15:31133600-31136400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr15:31133600-31136400	Enhancers	Fetal Thymus	thymus
23	chr15:31133600-31136600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr15:31133600-31136800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr15:31133800-31136200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr15:31133800-31136400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr15:31133800-31136400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:31133800-31136600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr15:31133800-31136800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr15:31134000-31136200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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