Variant report

Variant	rs2617236
Chromosome Location	chr15:42815733-42815734
allele	A/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	FOXA1	chr15:42815565-42815951	HepG2	liver:	n/a	chr15:42815690-42815705
2	FOXA2	chr15:42815522-42815833	HepG2	liver:	n/a	n/a
3	NR2F2	chr15:42815487-42815983	MCF-7	breast:	n/a	chr15:42815742-42815757
4	TCF7L2	chr15:42815556-42815942	PANC-1	pancreas:	n/a	n/a
5	FOXA1	chr15:42815552-42815931	HepG2	liver:	n/a	chr15:42815690-42815705
6	FOXA1	chr15:42815563-42815795	HepG2	liver:	n/a	chr15:42815690-42815705
7	FOXA1	chr15:42815423-42815935	HepG2	liver:	n/a	chr15:42815690-42815705

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42812167..42816411-chr15:42819043..42822094,4	K562	blood:

Variant related genes	Relation type
SNAP23	TF binding region
ENSG00000092531	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10454039	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1060291	0.90[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs10851410	0.95[CEU][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs10851411	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11022	0.95[CEU][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs11070374	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11631193	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11636577	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs11638208	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1197547	0.84[MKK][hapmap]
rs12324113	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12324717	0.95[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12898937	0.84[EUR][1000 genomes]
rs12903432	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12906697	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913324	0.84[EUR][1000 genomes]
rs1667493	0.82[AMR][1000 genomes]
rs1900920	0.84[EUR][1000 genomes]
rs1900921	0.95[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs2241998	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2255995	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412715	0.82[EUR][1000 genomes]
rs2595939	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2595940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2595941	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2617235	0.83[EUR][1000 genomes]
rs2617237	0.83[EUR][1000 genomes]
rs2617238	0.82[JPT][hapmap]
rs28886308	0.85[EUR][1000 genomes]
rs2899051	0.85[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs2899057	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34643746	0.86[EUR][1000 genomes]
rs3986280	0.95[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs4573906	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4923947	0.94[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs4923948	0.95[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs4924678	0.83[EUR][1000 genomes]
rs4924684	0.92[EUR][1000 genomes]
rs56357092	0.92[EUR][1000 genomes]
rs60380503	0.89[EUR][1000 genomes]
rs7168835	0.85[AMR][1000 genomes]
rs7169615	0.81[EUR][1000 genomes]
rs8033412	0.95[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs8034232	0.84[EUR][1000 genomes]
rs8034238	0.83[EUR][1000 genomes]
rs9302112	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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
2	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
3	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	esv2761870	chr15:42815733-42821267	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2617236	MAP1A	cis	parietal	SCAN
rs2617236	CXorf57	trans	parietal	SCAN
rs2617236	TMCO5A	cis	parietal	SCAN
rs2617236	SNAP23	cis	parietal	SCAN
rs2617236	INO80	cis	parietal	SCAN
rs2617236	TNPO2	trans	cerebellum	SCAN
rs2617236	TUBGCP4	cis	Skin Sun Exposed Lower leg	GTEx
rs2617236	CEP27	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42790800-42821400	Weak transcription	Right Ventricle	heart
2	chr15:42793000-42835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:42793800-42837200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:42797400-42839800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:42797600-42822200	Weak transcription	Small Intestine	intestine
6	chr15:42797600-42839400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:42799200-42839400	Weak transcription	Stomach Mucosa	stomach
8	chr15:42802400-42839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42802600-42817400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr15:42802800-42817200	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:42803200-42837200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:42803600-42839400	Weak transcription	A549	lung
13	chr15:42803800-42817600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:42804000-42826800	Strong transcription	HUVEC	blood vessel
15	chr15:42804600-42836400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr15:42804800-42817200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:42804800-42817400	Strong transcription	Adipose Nuclei	Adipose
18	chr15:42804800-42818000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:42804800-42818000	Strong transcription	Fetal Intestine Large	intestine
20	chr15:42804800-42825400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:42804800-42828800	Strong transcription	Placenta	Placenta
22	chr15:42804800-42836400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr15:42804800-42836400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr15:42805000-42818400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr15:42805000-42818800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:42805000-42818800	Strong transcription	NH-A	brain
27	chr15:42805200-42817000	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:42805200-42817600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:42805200-42825800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:42805400-42816600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:42805400-42816600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:42805400-42836800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:42805600-42818400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:42805600-42818800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:42806200-42836400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:42806200-42839000	Weak transcription	Fetal Brain Male	brain
37	chr15:42807200-42816600	Weak transcription	Pancreas	Pancrea
38	chr15:42807600-42821800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:42808200-42820400	Weak transcription	Brain Angular Gyrus	brain
40	chr15:42808200-42824800	Weak transcription	Hela-S3	cervix
41	chr15:42808400-42820000	Weak transcription	K562	blood
42	chr15:42808400-42821400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr15:42808400-42822000	Weak transcription	HMEC	breast
44	chr15:42808400-42839000	Weak transcription	Fetal Heart	heart
45	chr15:42808800-42821000	Weak transcription	Aorta	Aorta
46	chr15:42808800-42836000	Weak transcription	Esophagus	oesophagus
47	chr15:42810200-42816400	Weak transcription	Brain Substantia Nigra	brain
48	chr15:42810200-42831000	Weak transcription	Gastric	stomach
49	chr15:42810200-42840200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:42810400-42816200	Weak transcription	Brain Germinal Matrix	brain

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