Variant report

Variant	rs2470908
Chromosome Location	chr15:45028710-45028711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr15:45027602-45028744	GM12878	blood:	n/a	n/a
2	CREB1	chr15:45027574-45028754	GM12878	blood:	n/a	n/a
3	WRNIP1	chr15:45028625-45028830	GM12878	blood:	n/a	n/a
4	RUNX3	chr15:45027622-45028752	GM12878	blood:	n/a	n/a
5	IKZF1	chr15:45027490-45028886	GM12878	blood:	n/a	n/a
6	EP300	chr15:45027616-45028774	GM12878	blood:	n/a	chr15:45028524-45028533 chr15:45028664-45028678
7	RCOR1	chr15:45027656-45029007	IMR90	lung:	n/a	n/a
8	POLR2A	chr15:45027822-45028968	GM12892	blood:	n/a	n/a
9	RCOR1	chr15:45027564-45028880	K562	blood:	n/a	n/a
10	POLR2A	chr15:45028089-45028775	GM12878	blood:	n/a	n/a
11	TBP	chr15:45027923-45028731	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:45028683-45028878	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:45027828-45028759	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:45027788-45028789	GM12892	blood:	n/a	n/a
15	POLR2A	chr15:45026782-45029029	GM12891	blood:	n/a	n/a
16	POLR2A	chr15:45027954-45028748	GM12892	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B2M-1	chr15:45028681-45028760	NONHSAT042191

Variant related genes	Relation type
TRIM69	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10163110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10444818	0.86[ASN][1000 genomes]
rs1137516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11634059	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11634063	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11639157	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12912870	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1630168	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1669833	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1690313	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16974543	1.00[CEU][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs1720723	1.00[CEU][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs1720724	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1869125	0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1901530	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs1901538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1993152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1993153	0.92[ASN][1000 genomes]
rs2084835	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2167595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2468067	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2470913	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2960206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3100140	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3100141	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3110677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759881	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4923989	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs4923990	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4923991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4923993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62024991	0.81[EUR][1000 genomes]
rs62025968	1.00[EUR][1000 genomes]
rs62025969	0.97[EUR][1000 genomes]
rs6416439	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6416440	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493112	0.92[ASN][1000 genomes]
rs6493114	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493124	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493126	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6493127	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs6493128	1.00[EUR][1000 genomes]
rs7151	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165535	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7168090	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7172357	1.00[EUR][1000 genomes]
rs7172376	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7496437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7496559	0.94[EUR][1000 genomes]
rs7497862	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8035787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8036223	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8038532	0.97[EUR][1000 genomes]
rs935885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs935888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs935889	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases
2	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv832990	chr15:44990765-45162714	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2470908	METT5D1	trans	lymphoblastoid	seeQTL
rs2470908	TRIM69	cis	lymphoblastoid	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45022600-45028800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr15:45022800-45030800	Weak transcription	HUVEC	blood vessel
3	chr15:45024000-45031200	Weak transcription	HMEC	breast
4	chr15:45024200-45032200	Weak transcription	Right Atrium	heart
5	chr15:45024400-45028800	Weak transcription	Lung	lung
6	chr15:45024400-45031200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:45025000-45030800	Weak transcription	Brain Angular Gyrus	brain
8	chr15:45025000-45030800	Weak transcription	Brain Anterior Caudate	brain
9	chr15:45026000-45029000	Enhancers	Primary B cells from peripheral blood	blood
10	chr15:45026400-45029000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr15:45026400-45029000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:45026600-45028800	Enhancers	Primary T cells from cord blood	blood
13	chr15:45026600-45029000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:45026600-45029200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr15:45026800-45029600	Enhancers	Primary B cells from cord blood	blood
16	chr15:45027000-45028800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:45027000-45029000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr15:45027000-45029000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:45027000-45029000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr15:45027200-45029000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:45027200-45029000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr15:45027200-45029000	Enhancers	Colon Smooth Muscle	Colon
23	chr15:45027200-45030800	Weak transcription	Brain Substantia Nigra	brain
24	chr15:45027600-45028800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr15:45027600-45028800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr15:45027600-45029000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:45027600-45029800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr15:45027600-45029800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr15:45027800-45028800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:45027800-45028800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr15:45027800-45029000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:45027800-45029000	Flanking Active TSS	GM12878-XiMat	blood
33	chr15:45028000-45028800	Active TSS	Duodenum Mucosa	Duodenum
34	chr15:45028200-45029000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:45028400-45028800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:45028400-45029000	Enhancers	Brain Hippocampus Middle	brain
37	chr15:45028400-45029800	Weak transcription	Placenta	Placenta
38	chr15:45028600-45028800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:45028600-45028800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:45028600-45028800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr15:45028600-45029000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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