Variant report

Variant	rs1901530
Chromosome Location	chr15:45005146-45005147
allele	A/G
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	MAX	chr15:45003327-45005151	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:45002354-45013577	GM18951	blood:	n/a	n/a
3	MAX	chr15:45003207-45005188	SK-N-SH	brain:	n/a	n/a
4	PAX5	chr15:45004728-45005413	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:45002647-45005444	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr15:45002280-45010248	GM12891	blood:	n/a	n/a
7	YY1	chr15:45004734-45005432	K562	blood:	n/a	n/a
8	POLR2A	chr15:45004542-45005230	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr15:45004585-45005229	K562	blood:	n/a	n/a
10	POLR2A	chr15:45002339-45005459	K562	blood:	n/a	n/a
11	POLR2A	chr15:45002253-45014109	GM12892	blood:	n/a	n/a
12	WRNIP1	chr15:45002331-45005445	GM12878	blood:	n/a	n/a
13	BCLAF1	chr15:45002272-45005506	GM12878	blood:	n/a	chr15:45003027-45003040 chr15:45003589-45003598 chr15:45003959-45003972 chr15:45003029-45003038 chr15:45005259-45005267 chr15:45003577-45003586 chr15:45004128-45004137
14	FOXM1	chr15:45002235-45005519	GM12878	blood:	n/a	n/a
15	POU2F2	chr15:45004664-45005222	GM12891	blood:	n/a	n/a
16	POLR2A	chr15:45002358-45005169	K562	blood:	n/a	n/a
17	PAX5	chr15:45004698-45005333	GM12878	blood:	n/a	n/a
18	POLR2A	chr15:45002760-45005424	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr15:45002255-45010226	GM12891	blood:	n/a	n/a
20	PAX5	chr15:45004938-45005286	GM12892	blood:	n/a	n/a
21	TCF12	chr15:45004662-45005192	A549	lung:	n/a	chr15:45004892-45004899
22	POLR2A	chr15:45003220-45005427	GM12878	blood:	n/a	n/a
23	UBTF	chr15:45003209-45005150	K562	blood:	n/a	n/a
24	TBL1XR1	chr15:45002321-45008799	GM12878	blood:	n/a	n/a
25	GATA1	chr15:45002260-45005291	PBDE	blood:	n/a	chr15:45002520-45002529
26	MAX	chr15:45003163-45005246	K562	blood:	n/a	n/a
27	POLR2A	chr15:45002045-45013680	GM18505	blood:	n/a	n/a
28	POU2F2	chr15:45004566-45005156	GM12878	blood:	n/a	n/a
29	NR2F2	chr15:45003175-45005294	K562	blood:	n/a	n/a
30	POLR2A	chr15:45002139-45014682	GM12878	blood:	n/a	n/a
31	REST	chr15:45004796-45005174	GM12878	blood:	n/a	n/a
32	BHLHE40	chr15:45002348-45005461	GM12878	blood:	n/a	n/a
33	RCOR1	chr15:45002143-45005160	K562	blood:	n/a	n/a
34	POLR2A	chr15:45002322-45013693	GM19193	blood:	n/a	n/a
35	POLR2A	chr15:45002218-45005514	HL-60	blood:	n/a	n/a
36	NFIC	chr15:45004443-45005252	SK-N-SH	brain:	n/a	n/a
37	BCLAF1	chr15:45002327-45005451	GM12878	blood:	n/a	chr15:45003027-45003040 chr15:45003589-45003598 chr15:45003959-45003972 chr15:45003029-45003038 chr15:45005259-45005267 chr15:45003577-45003586 chr15:45004128-45004137
38	RUNX3	chr15:45002181-45005194	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:45002192-45013674	GM12891	blood:	n/a	n/a
40	UBTF	chr15:45004678-45005279	K562	blood:	n/a	n/a
41	MAX	chr15:45003194-45005198	A549	lung:	n/a	n/a
42	RFX5	chr15:45001383-45006423	SK-N-SH	brain:	n/a	chr15:45003663-45003672
43	POLR2A	chr15:45002796-45006154	MCF10A-Er-Src	breast:	n/a	n/a
44	MYC	chr15:45002437-45005162	K562	blood:	n/a	n/a
45	YY1	chr15:45004647-45005446	GM12892	blood:	n/a	n/a
46	MYC	chr15:45004700-45005300	MCF10A-Er-Src	breast:	n/a	n/a
47	MYC	chr15:45004273-45005329	MCF10A-Er-Src	breast:	n/a	n/a
48	SIN3A	chr15:45005063-45005425	GM12878	blood:	n/a	n/a
49	POLR2A	chr15:45002251-45013700	GM19099	blood:	n/a	n/a
50	YY1	chr15:45004573-45005291	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:21112938..21114460-chr15:45004450..45006409,2	K562	blood:
2	chr15:45004559..45007244-chr15:45019568..45021417,3	MCF-7	breast:
3	chr15:44951739..44957508-chr15:45000588..45008057,33	K562	blood:
4	chr15:44980888..44990623-chr15:45002366..45006726,14	K562	blood:
5	chr15:44952988..44962373-chr15:45002018..45007307,26	MCF-7	breast:
6	chr15:44968315..44970113-chr15:45003699..45005679,2	MCF-7	breast:
7	chr15:44968819..44972092-chr15:45002551..45007992,5	K562	blood:
8	chr15:45000863..45005844-chr15:45018710..45023352,9	MCF-7	breast:
9	chr15:44951575..44958275-chr15:45001046..45006983,19	MCF-7	breast:
10	chr15:44952188..44965604-chr15:45001074..45012963,51	K562	blood:

Variant related genes	Relation type
PATL2	TF binding region
B2M	TF binding region
ENSG00000229474	Chromatin interaction
ENSG00000206957	Chromatin interaction
ENSG00000185880	Chromatin interaction
ENSG00000104133	Chromatin interaction
ENSG00000127483	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10163110	0.82[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10444818	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1137516	0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs11634059	0.81[EUR][1000 genomes]
rs11634063	0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs11639157	0.81[EUR][1000 genomes]
rs12912870	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1630168	0.87[EUR][1000 genomes]
rs1669833	0.87[EUR][1000 genomes]
rs1690313	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];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16974543	1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs1720723	1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs1720724	0.87[EUR][1000 genomes]
rs1869125	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1901538	0.81[EUR][1000 genomes]
rs1993152	0.82[CHB][hapmap]
rs2084835	0.82[CHB][hapmap]
rs2167595	0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2468067	0.81[EUR][1000 genomes]
rs2470908	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]
rs2960206	0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs3100140	0.81[EUR][1000 genomes]
rs3100141	0.86[CHD][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs3110677	0.81[EUR][1000 genomes]
rs3759878	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs3759881	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4923989	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs4923990	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4923991	0.81[EUR][1000 genomes]
rs4923993	0.82[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs62024991	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62025968	0.81[EUR][1000 genomes]
rs62025969	0.84[EUR][1000 genomes]
rs6416439	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6416440	0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs6493110	0.90[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6493111	1.00[ASW][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6493114	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493116	0.81[EUR][1000 genomes]
rs6493118	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493119	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs6493124	0.81[EUR][1000 genomes]
rs6493125	0.89[CHB][hapmap];0.81[EUR][1000 genomes]
rs6493126	0.81[EUR][1000 genomes]
rs6493127	1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs6493128	0.81[EUR][1000 genomes]
rs7151	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7165535	0.82[CHB][hapmap]
rs7168090	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7172357	0.81[EUR][1000 genomes]
rs7172376	0.81[EUR][1000 genomes]
rs7496437	0.82[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7496559	0.87[EUR][1000 genomes]
rs7497862	0.82[AMR][1000 genomes]
rs8035787	0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8036223	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8038532	0.84[EUR][1000 genomes]
rs935885	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs935888	0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs935889	0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1901530	METT5D1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45001400-45005200	Active TSS	GM12878-XiMat	blood
2	chr15:45002000-45005600	Active TSS	Colon Smooth Muscle	Colon
3	chr15:45002000-45005800	Active TSS	Brain Anterior Caudate	brain
4	chr15:45002000-45006000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr15:45002200-45005800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr15:45002200-45006800	Active TSS	Colonic Mucosa	Colon
7	chr15:45002400-45005400	Active TSS	Brain Cingulate Gyrus	brain
8	chr15:45002400-45005400	Active TSS	Spleen	Spleen
9	chr15:45002400-45005600	Active TSS	Rectal Smooth Muscle	rectum
10	chr15:45002400-45005600	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr15:45002400-45006000	Active TSS	NHLF	lung
12	chr15:45002400-45006400	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr15:45002400-45006600	Active TSS	Lung	lung
14	chr15:45002400-45006600	Active TSS	Stomach Smooth Muscle	stomach
15	chr15:45002400-45006800	Active TSS	Small Intestine	intestine
16	chr15:45002400-45007000	Active TSS	Left Ventricle	heart
17	chr15:45002400-45007200	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr15:45002400-45007200	Active TSS	Right Ventricle	heart
19	chr15:45002600-45005200	Active TSS	Muscle Satellite Cultured Cells	--
20	chr15:45002600-45005200	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr15:45002600-45005200	Active TSS	Osteobl	bone
22	chr15:45002600-45005400	Active TSS	HSMM	muscle
23	chr15:45002600-45005600	Active TSS	NHEK	skin
24	chr15:45002600-45005800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:45002600-45005800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:45002600-45005800	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr15:45002600-45006200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:45002600-45006200	Active TSS	Duodenum Mucosa	Duodenum
29	chr15:45002600-45006400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:45002600-45007200	Active TSS	Psoas Muscle	Psoas
31	chr15:45002800-45005200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:45002800-45005200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:45002800-45005200	Active TSS	HMEC	breast
34	chr15:45002800-45005200	Active TSS	K562	blood
35	chr15:45002800-45005200	Active TSS	NH-A	brain
36	chr15:45002800-45005400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:45002800-45005400	Active TSS	Aorta	Aorta
38	chr15:45002800-45005400	Active TSS	Brain Substantia Nigra	brain
39	chr15:45002800-45005400	Active TSS	Fetal Kidney	kidney
40	chr15:45002800-45005600	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr15:45002800-45005600	Active TSS	Primary monocytes fromperipheralblood	blood
42	chr15:45002800-45005600	Active TSS	Primary T cells from cord blood	blood
43	chr15:45002800-45005600	Active TSS	Fetal Thymus	thymus
44	chr15:45002800-45005600	Active TSS	Thymus	Thymus
45	chr15:45002800-45005600	Active TSS	A549	lung
46	chr15:45002800-45005800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr15:45002800-45005800	Active TSS	Brain Angular Gyrus	brain
48	chr15:45002800-45005800	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr15:45002800-45006000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:45002800-45006200	Active TSS	NHDF-Ad	bronchial

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