Variant report

Variant	rs7086
Chromosome Location	chr15:42451108-42451109
allele	C/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	POLR2A	chr15:42451073-42451739	GM12891	blood:	n/a	n/a
2	POLR2A	chr15:42449741-42452236	K562	blood:	n/a	n/a
3	POLR2A	chr15:42450934-42451394	GM12891	blood:	n/a	n/a
4	JUN	chr15:42450208-42451257	K562	blood:	n/a	n/a
5	GATA3	chr15:42450378-42451293	SK-N-SH	brain:	n/a	chr15:42450881-42450892 chr15:42450836-42450849
6	GATA3	chr15:42450220-42451334	SK-N-SH	brain:	n/a	chr15:42450881-42450892 chr15:42450836-42450849
7	POLR2A	chr15:42451065-42451422	GM12892	blood:	n/a	n/a
8	MYC	chr15:42450532-42451175	K562	blood:	n/a	n/a
9	MAX	chr15:42450565-42451117	K562	blood:	n/a	n/a
10	POLR2A	chr15:42451024-42451488	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:42442020..42443791-chr15:42450046..42452930,2	K562	blood:
2	chr15:42449739..42452702-chr15:42454816..42457885,4	K562	blood:
3	chr15:42375390..42378323-chr15:42449253..42451439,2	K562	blood:
4	chr15:42450192..42452285-chr15:42459355..42462158,2	K562	blood:
5	chr15:42441690..42443791-chr15:42450046..42452930,3	K562	blood:
6	chr15:42426456..42429397-chr15:42449787..42451841,2	MCF-7	breast:

Variant related genes	Relation type
PLA2G4F	TF binding region
ENSG00000159337	Chromatin interaction
ENSG00000166887	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10775126	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[EUR][1000 genomes]
rs10851407	0.80[EUR][1000 genomes]
rs10851408	0.80[EUR][1000 genomes]
rs10851409	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs11070370	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs11631917	0.80[EUR][1000 genomes]
rs11631983	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs12441642	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12594162	0.80[EUR][1000 genomes]
rs12917101	0.80[EUR][1000 genomes]
rs1619030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1624183	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1659212	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs1659213	0.83[CHB][hapmap]
rs1659218	0.83[CHB][hapmap]
rs1659219	0.82[CHB][hapmap]
rs1659222	0.82[CHB][hapmap]
rs1678985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1678986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1678991	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1678992	0.83[CHB][hapmap]
rs1678993	0.83[CHB][hapmap]
rs1679002	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1679009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1679010	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1679012	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes]
rs1703750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1703754	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1703755	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1712418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1712421	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2138831	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2289295	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs2412682	0.80[EUR][1000 genomes]
rs2412685	0.80[EUR][1000 genomes]
rs2620386	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs2918459	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs2918460	0.83[CHB][hapmap]
rs2918461	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs3743006	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs4329897	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs4923940	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[EUR][1000 genomes]
rs4923943	0.80[EUR][1000 genomes]
rs4924645	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[EUR][1000 genomes]
rs4924648	0.80[EUR][1000 genomes]
rs4924653	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs4924658	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[EUR][1000 genomes]
rs4924660	0.80[EUR][1000 genomes]
rs598360	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs622442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs622714	0.99[ASN][1000 genomes]
rs624841	0.99[ASN][1000 genomes]
rs633934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6493027	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[EUR][1000 genomes]
rs660126	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs677878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs678778	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs681029	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7179709	0.83[CHB][hapmap]
rs7181742	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs7183015	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs7183546	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs8024732	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs8025601	1.00[CEU][hapmap]
rs8031315	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs8033080	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8036046	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8036187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8036596	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs8037020	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs9672382	0.85[EUR][1000 genomes]
rs9920921	1.00[CEU][hapmap];0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv9245	chr15:42441849-42453572	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7086	ENSG00000166887	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42436000-42452000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:42439400-42451200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:42439400-42451800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:42444000-42451600	Weak transcription	HUVEC	blood vessel
5	chr15:42444800-42451200	Weak transcription	Aorta	Aorta
6	chr15:42445000-42451400	Weak transcription	Brain Angular Gyrus	brain
7	chr15:42446600-42451200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:42447800-42451400	Weak transcription	Fetal Lung	lung
9	chr15:42448200-42451200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr15:42448200-42453000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:42448400-42452400	Weak transcription	Fetal Kidney	kidney
12	chr15:42448600-42451400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:42448600-42452800	Weak transcription	Hela-S3	cervix
14	chr15:42448600-42453800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:42448800-42451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:42448800-42451400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:42448800-42452200	Weak transcription	Small Intestine	intestine
18	chr15:42449000-42451200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:42449000-42451400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:42449000-42452200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:42449000-42452400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:42449000-42481800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr15:42449200-42451200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr15:42449200-42451200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr15:42449200-42452400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:42449200-42453800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:42449200-42456000	Weak transcription	Stomach Mucosa	stomach
28	chr15:42449400-42451600	Weak transcription	Dnd41	blood
29	chr15:42449400-42451800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:42449600-42451200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr15:42449600-42451200	Weak transcription	Ovary	ovary
32	chr15:42449600-42452200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:42449600-42468200	Strong transcription	Fetal Brain Female	brain
34	chr15:42449800-42451400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr15:42449800-42452200	Enhancers	Left Ventricle	heart
36	chr15:42450000-42451200	Enhancers	Brain Hippocampus Middle	brain
37	chr15:42450200-42451200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:42450200-42451600	Enhancers	Placenta Amnion	Placenta Amnion
39	chr15:42450200-42451600	Enhancers	NH-A	brain
40	chr15:42450200-42452000	Genic enhancers	Esophagus	oesophagus
41	chr15:42450200-42468600	Strong transcription	Fetal Stomach	stomach
42	chr15:42450200-42472400	Strong transcription	Fetal Intestine Small	intestine
43	chr15:42450400-42451200	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr15:42450400-42451200	Genic enhancers	Osteobl	bone
45	chr15:42450400-42451400	Enhancers	NHDF-Ad	bronchial
46	chr15:42450400-42451800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:42450400-42452200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr15:42450400-42457000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:42450400-42468400	Strong transcription	Primary T cells from cord blood	blood
50	chr15:42450400-42468400	Strong transcription	Fetal Muscle Trunk	muscle

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