Variant report

Variant	rs4923993
Chromosome Location	chr15:45026900-45026901
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	SPI1	chr15:45026716-45026968	GM12891	blood:	n/a	n/a
2	POLR2A	chr15:45026782-45029029	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45017745..45022716-chr15:45023664..45026968,5	MCF-7	breast:
2	chr15:45023381..45025448-chr15:45025750..45028382,2	K562	blood:

Variant related genes	Relation type
TRIM69	TF binding region
ENSG00000185880	Chromatin interaction

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];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10444818	0.90[ASN][1000 genomes]
rs1137516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634059	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11634063	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11639157	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12912870	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[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];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];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];0.96[ASN][1000 genomes]
rs1901530	0.82[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs1901538	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1993152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1993153	0.96[ASN][1000 genomes]
rs2084835	1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs2167595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468067	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2470908	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]
rs2470913	0.80[ASN][1000 genomes]
rs2960206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3100140	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3100141	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3110677	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759881	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4923989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs4923990	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4923991	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62024991	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62025968	1.00[EUR][1000 genomes]
rs62025969	0.97[EUR][1000 genomes]
rs6416439	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6416440	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493112	0.96[ASN][1000 genomes]
rs6493114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493116	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493126	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[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];0.96[ASN][1000 genomes]
rs7165535	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7168090	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7172357	1.00[EUR][1000 genomes]
rs7172376	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7496437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7496559	0.94[EUR][1000 genomes]
rs7497862	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8035787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8036223	0.94[EUR][1000 genomes];0.97[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];0.96[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];1.00[ASN][1000 genomes]
rs935889	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs4923993	METT5D1	trans	lymphoblastoid	seeQTL
rs4923993	TRIM69	cis	lymphoblastoid	seeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45022200-45027200	Weak transcription	Aorta	Aorta
2	chr15:45022200-45027600	Weak transcription	Colonic Mucosa	Colon
3	chr15:45022200-45027800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:45022200-45027800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:45022400-45027800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr15:45022400-45027800	Weak transcription	Placenta	Placenta
7	chr15:45022400-45028000	Weak transcription	Psoas Muscle	Psoas
8	chr15:45022600-45027200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:45022600-45028000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:45022600-45028800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:45022800-45028000	Weak transcription	Fetal Kidney	kidney
12	chr15:45022800-45030800	Weak transcription	HUVEC	blood vessel
13	chr15:45023000-45027000	Weak transcription	Brain Substantia Nigra	brain
14	chr15:45023000-45027000	Weak transcription	NHDF-Ad	bronchial
15	chr15:45023000-45027200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:45023000-45027200	Weak transcription	NHLF	lung
17	chr15:45023000-45027600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:45023000-45028000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:45023200-45027200	Weak transcription	Fetal Intestine Small	intestine
20	chr15:45023200-45027800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:45023400-45027200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr15:45023800-45027200	Weak transcription	Hela-S3	cervix
23	chr15:45024000-45027200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:45024000-45027800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:45024000-45031200	Weak transcription	HMEC	breast
26	chr15:45024200-45027200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:45024200-45027200	Weak transcription	Dnd41	blood
28	chr15:45024200-45027800	Weak transcription	Fetal Stomach	stomach
29	chr15:45024200-45027800	Weak transcription	Thymus	Thymus
30	chr15:45024200-45028000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:45024200-45032200	Weak transcription	Right Atrium	heart
32	chr15:45024400-45027200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:45024400-45027200	Weak transcription	Colon Smooth Muscle	Colon
34	chr15:45024400-45027200	Weak transcription	Fetal Heart	heart
35	chr15:45024400-45027200	Weak transcription	Ovary	ovary
36	chr15:45024400-45027600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:45024400-45028200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:45024400-45028200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:45024400-45028400	Weak transcription	Brain Hippocampus Middle	brain
40	chr15:45024400-45028800	Weak transcription	Lung	lung
41	chr15:45024400-45031200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:45024600-45027000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr15:45024600-45027200	Weak transcription	Adipose Nuclei	Adipose
44	chr15:45024600-45027200	Weak transcription	Fetal Lung	lung
45	chr15:45024600-45027600	Weak transcription	HSMM	muscle
46	chr15:45024600-45027800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:45024600-45027800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr15:45024600-45027800	Weak transcription	Liver	Liver
49	chr15:45024800-45027000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr15:45024800-45027200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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