Variant report

Variant	rs3784390
Chromosome Location	chr15:39871080-39871081
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	TAL1	chr15:39870976-39871254	K562	blood:	n/a	n/a
2	POLR2A	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
3	CTCF	chr15:39871080-39871230	A549	lung:	n/a	n/a
4	GATA2	chr15:39870911-39872650	HUVEC	blood vessel:	n/a	chr15:39871069-39871085 chr15:39872609-39872619 chr15:39871069-39871085 chr15:39871089-39871106
5	POLR2A	chr15:39870845-39871164	HUVEC	blood vessel:	n/a	n/a
6	MAZ	chr15:39870877-39886058	IMR90	lung:	n/a	chr15:39874192-39874207 chr15:39872697-39872706 chr15:39873005-39873014
7	POLR2A	chr15:39870931-39871186	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr15:39870574-39892778	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr15:39870584-39871471	H1-hESC	embryonic stem cell:	n/a	n/a
10	SMC3	chr15:39870801-39874615	SK-N-SH	brain:	n/a	chr15:39873146-39873160 chr15:39872057-39872071
11	POLR2A	chr15:39870624-39892458	HUVEC	blood vessel:	n/a	n/a
12	MXI1	chr15:39870632-39876677	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:39869407..39871427-chr15:39874178..39876262,2	K562	blood:
2	chr15:39869319..39871177-chr15:39871544..39874678,3	MCF-7	breast:
3	chr15:39867115..39869175-chr15:39869428..39872036,2	MCF-7	breast:
4	chr15:39869641..39872520-chr15:39877889..39880142,2	K562	blood:

Variant related genes	Relation type
THBS1	TF binding region
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1004739	1.00[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs1004740	1.00[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs1004741	0.92[EUR][1000 genomes]
rs10520135	0.87[CEU][hapmap]
rs10520137	1.00[CEU][hapmap]
rs11070220	1.00[CEU][hapmap]
rs11070222	1.00[CEU][hapmap]
rs11070223	1.00[CEU][hapmap]
rs11070225	1.00[CEU][hapmap]
rs1134485	1.00[CEU][hapmap]
rs11630406	1.00[CEU][hapmap]
rs11631570	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs11632879	1.00[CEU][hapmap]
rs11633974	1.00[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs11635103	1.00[CEU][hapmap]
rs11638041	1.00[CEU][hapmap]
rs11638500	1.00[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs11852591	1.00[CEU][hapmap]
rs11852649	1.00[CEU][hapmap]
rs11854797	1.00[CEU][hapmap]
rs11856294	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11856971	1.00[CEU][hapmap]
rs11857819	1.00[CEU][hapmap]
rs11857927	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12908846	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12912082	1.00[CEU][hapmap]
rs16969386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[YRI][hapmap]
rs16969410	1.00[CEU][hapmap]
rs16969445	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16969459	1.00[CEU][hapmap]
rs16969460	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs16969475	1.00[CEU][hapmap]
rs16969478	1.00[CEU][hapmap]
rs16969495	0.88[CHB][hapmap]
rs1876853	1.00[CEU][hapmap]
rs2228261	1.00[CEU][hapmap]
rs2292304	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2292305	1.00[CEU][hapmap]
rs2411312	0.81[TSI][hapmap]
rs2411313	1.00[CEU][hapmap]
rs2412409	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2412410	0.92[EUR][1000 genomes]
rs2412411	0.92[EUR][1000 genomes]
rs2412413	1.00[CEU][hapmap]
rs2412415	1.00[CEU][hapmap]
rs2412417	1.00[CEU][hapmap]
rs2412419	1.00[CEU][hapmap]
rs2898686	1.00[CEU][hapmap]
rs2898687	1.00[CEU][hapmap]
rs2898688	1.00[CEU][hapmap]
rs34275067	0.81[EUR][1000 genomes]
rs35754803	0.80[EUR][1000 genomes]
rs4349120	1.00[CEU][hapmap]
rs4476147	1.00[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4547308	1.00[CEU][hapmap]
rs4583211	1.00[CEU][hapmap]
rs56722485	0.92[EUR][1000 genomes]
rs57969006	0.92[EUR][1000 genomes]
rs58332880	0.80[EUR][1000 genomes]
rs60884629	0.89[EUR][1000 genomes]
rs7162070	1.00[CEU][hapmap]
rs7162781	1.00[CEU][hapmap]
rs7167184	1.00[CEU][hapmap]
rs7168755	1.00[CEU][hapmap]
rs7169478	1.00[CEU][hapmap]
rs7169574	1.00[CEU][hapmap]
rs72725045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753599	1.00[CEU][hapmap]
rs8029602	1.00[CEU][hapmap]
rs8032035	1.00[CEU][hapmap]
rs8036376	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[YRI][hapmap]
rs8036633	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs884584	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39851000-39871800	Weak transcription	Pancreas	Pancrea
2	chr15:39863600-39871200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:39865800-39871200	Weak transcription	Esophagus	oesophagus
4	chr15:39866000-39871200	Weak transcription	Adipose Nuclei	Adipose
5	chr15:39866800-39871200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:39869600-39871200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:39869600-39871400	Enhancers	HSMM	muscle
8	chr15:39870000-39871600	Enhancers	Fetal Lung	lung
9	chr15:39870400-39871200	Enhancers	HUVEC	blood vessel
10	chr15:39870400-39871600	Enhancers	Fetal Stomach	stomach
11	chr15:39870600-39871200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
12	chr15:39870600-39871200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr15:39870600-39871200	Enhancers	NHDF-Ad	bronchial
14	chr15:39870600-39871200	Enhancers	Osteobl	bone
15	chr15:39870600-39871400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr15:39870600-39871400	Enhancers	HSMMtube	muscle
17	chr15:39870600-39871400	Enhancers	NHEK	skin
18	chr15:39870600-39871600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr15:39870600-39871600	Enhancers	Fetal Kidney	kidney
20	chr15:39870600-39871600	Enhancers	HMEC	breast
21	chr15:39870600-39872000	Enhancers	Fetal Heart	heart
22	chr15:39870800-39871200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:39870800-39871200	Enhancers	Fetal Brain Male	brain
24	chr15:39870800-39871400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
25	chr15:39870800-39871400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:39870800-39871400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:39870800-39871400	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr15:39870800-39871400	Enhancers	Fetal Brain Female	brain
29	chr15:39870800-39871400	Enhancers	A549	lung
30	chr15:39870800-39871400	Enhancers	NH-A	brain
31	chr15:39870800-39871600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr15:39870800-39871600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:39870800-39871600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:39870800-39871600	Enhancers	Colon Smooth Muscle	Colon
35	chr15:39870800-39871600	Enhancers	Ovary	ovary
36	chr15:39870800-39871600	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr15:39870800-39871800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:39870800-39871800	Enhancers	Fetal Muscle Leg	muscle
39	chr15:39870800-39871800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr15:39870800-39872000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:39871000-39871200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:39871000-39871200	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr15:39871000-39871200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:39871000-39871200	Enhancers	Stomach Smooth Muscle	stomach
45	chr15:39871000-39871400	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr15:39871000-39871400	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:39871000-39871400	Enhancers	NHLF	lung
48	chr15:39871000-39871600	Enhancers	H1 Cell Line	embryonic stem cell
49	chr15:39871000-39871600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
50	chr15:39871000-39871600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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