Variant report

Variant	rs2595940
Chromosome Location	chr15:42793371-42793372
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42786349..42789071-chr15:42793305..42795618,2	K562	blood:
2	chr15:42786351..42790033-chr15:42790160..42794805,5	K562	blood:
3	chr15:42792525..42795008-chr15:42866851..42868814,2	K562	blood:

Variant related genes	Relation type
ENSG00000092531	Chromatin interaction
ENSG00000159433	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10454039	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1060291	0.90[CEU][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs10851410	0.95[CEU][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs10851411	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11022	0.95[CEU][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs11070374	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11631193	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11636577	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs11638208	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1197547	0.84[MKK][hapmap]
rs12324113	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12324717	0.95[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs12898937	0.82[EUR][1000 genomes]
rs12903432	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906697	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12913324	0.87[EUR][1000 genomes]
rs1900920	0.83[EUR][1000 genomes]
rs1900921	0.95[CEU][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs2241998	1.00[ASW][hapmap];0.95[CEU][hapmap];0.84[CHD][hapmap];0.86[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];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2255995	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412715	0.81[EUR][1000 genomes]
rs2595939	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595941	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617235	0.82[EUR][1000 genomes]
rs2617236	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]
rs2617237	0.82[EUR][1000 genomes]
rs2617238	0.82[JPT][hapmap]
rs28886308	0.88[EUR][1000 genomes]
rs2899051	0.85[CEU][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes]
rs2899057	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34643746	0.89[EUR][1000 genomes]
rs3986280	0.95[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs4573906	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923947	0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs4923948	0.95[CEU][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs4924678	0.81[EUR][1000 genomes]
rs4924684	0.95[EUR][1000 genomes]
rs56357092	0.95[EUR][1000 genomes]
rs60380503	0.92[EUR][1000 genomes]
rs7168835	0.82[AMR][1000 genomes]
rs7169615	0.84[EUR][1000 genomes]
rs8033412	0.95[CEU][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs8034232	0.83[EUR][1000 genomes]
rs8034238	0.82[EUR][1000 genomes]
rs9302112	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2595940	INO80	cis	parietal	SCAN
rs2595940	SNAP23	cis	parietal	SCAN
rs2595940	CEP27	Cis_1M	lymphoblastoid	RTeQTL
rs2595940	TNPO2	trans	cerebellum	SCAN
rs2595940	TMCO5A	cis	parietal	SCAN
rs2595940	TUBGCP4	cis	Skin Sun Exposed Lower leg	GTEx
rs2595940	CXorf57	trans	parietal	SCAN
rs2595940	MAP1A	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42788400-42808000	Weak transcription	Esophagus	oesophagus
2	chr15:42788600-42798400	Weak transcription	Ovary	ovary
3	chr15:42788600-42805600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:42788600-42806600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:42788600-42807200	Weak transcription	Fetal Kidney	kidney
6	chr15:42788800-42793600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:42788800-42797000	Weak transcription	HSMMtube	muscle
8	chr15:42788800-42800400	Weak transcription	Fetal Lung	lung
9	chr15:42788800-42805200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:42788800-42805400	Weak transcription	Brain Germinal Matrix	brain
11	chr15:42789000-42794000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:42789000-42797000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:42789000-42797000	Weak transcription	Brain Angular Gyrus	brain
14	chr15:42789000-42803400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:42789000-42805400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:42789000-42806400	Weak transcription	Thymus	Thymus
17	chr15:42789200-42794000	Enhancers	Placenta	Placenta
18	chr15:42789200-42796800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:42789200-42798400	Weak transcription	Primary T cells from cord blood	blood
20	chr15:42789200-42800600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:42789200-42802400	Weak transcription	Fetal Brain Female	brain
22	chr15:42789200-42804400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:42789200-42805800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:42789200-42806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:42789600-42793800	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr15:42790200-42793800	Strong transcription	Fetal Stomach	stomach
27	chr15:42790200-42793800	Enhancers	Pancreas	Pancrea
28	chr15:42790200-42794200	Enhancers	Adipose Nuclei	Adipose
29	chr15:42790400-42802600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:42790600-42797200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr15:42790600-42800200	Weak transcription	Psoas Muscle	Psoas
32	chr15:42790600-42805200	Weak transcription	Dnd41	blood
33	chr15:42790600-42806600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr15:42790600-42807200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr15:42790800-42793600	Enhancers	Stomach Mucosa	stomach
36	chr15:42790800-42794000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr15:42790800-42795800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:42790800-42797200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr15:42790800-42798400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:42790800-42805000	Weak transcription	Fetal Thymus	thymus
41	chr15:42790800-42809800	Weak transcription	Spleen	Spleen
42	chr15:42790800-42810000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr15:42790800-42821400	Weak transcription	Right Ventricle	heart
44	chr15:42791000-42793400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr15:42791000-42794200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:42791200-42796800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:42791200-42803800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr15:42791200-42809800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:42791400-42794000	Genic enhancers	Primary B cells from peripheral blood	blood
50	chr15:42791400-42796600	Enhancers	Monocytes-CD14+_RO01746	blood

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