Variant report

Variant	rs2593280
Chromosome Location	chr15:76150965-76150966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76134245..76136824-chr15:76150305..76152111,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140367	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12910576	0.87[AMR][1000 genomes]
rs12915012	0.84[AMR][1000 genomes]
rs1391894	0.93[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs1695378	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs184580	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs189197	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255701	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2441929	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2455899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460798	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2460800	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2469039	0.93[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2593277	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2593278	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28876229	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2959852	0.80[EUR][1000 genomes]
rs334930	0.93[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap]
rs334934	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs335681	1.00[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs335697	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs335706	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs335711	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886747	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886753	1.00[ASW][hapmap];0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4886754	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71403522	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8024155	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs985849	1.00[ASW][hapmap];0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1044733	chr15:76120924-76228880	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv974601	chr15:76139204-76160467	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2593280	LRRC49	cis	cerebellum	SCAN
rs2593280	NRG4	cis	cerebellum	SCAN
rs2593280	UBE2Q2	cis	Liver	GTEx
rs2593280	UBE2Q2	cis	multi-tissue	Pritchard
rs2593280	NRG4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76137200-76166200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:76137600-76155400	Weak transcription	Stomach Mucosa	stomach
3	chr15:76137600-76165000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:76137800-76152400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:76137800-76165800	Weak transcription	Liver	Liver
6	chr15:76137800-76166000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:76137800-76188400	Weak transcription	Brain Anterior Caudate	brain
8	chr15:76138000-76151000	Weak transcription	Primary B cells from cord blood	blood
9	chr15:76138000-76179600	Weak transcription	Small Intestine	intestine
10	chr15:76138200-76153600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:76138200-76154000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:76138200-76154200	Weak transcription	Gastric	stomach
13	chr15:76138200-76154200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:76138200-76154200	Weak transcription	Right Atrium	heart
15	chr15:76138200-76161800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:76138200-76166000	Weak transcription	Aorta	Aorta
17	chr15:76138200-76166000	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:76138200-76166000	Weak transcription	Pancreas	Pancrea
19	chr15:76138200-76166000	Weak transcription	Spleen	Spleen
20	chr15:76138200-76183000	Weak transcription	Hela-S3	cervix
21	chr15:76138200-76195200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:76138200-76195400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:76138400-76153000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr15:76138400-76153000	Weak transcription	Thymus	Thymus
25	chr15:76138400-76155000	Weak transcription	NH-A	brain
26	chr15:76138400-76184000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:76138800-76166000	Weak transcription	Esophagus	oesophagus
28	chr15:76138800-76169200	Weak transcription	Psoas Muscle	Psoas
29	chr15:76139400-76152400	Weak transcription	NHDF-Ad	bronchial
30	chr15:76139400-76153200	Weak transcription	Placenta	Placenta
31	chr15:76140000-76156600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:76140000-76161800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr15:76140000-76165800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr15:76140000-76184000	Weak transcription	Fetal Kidney	kidney
35	chr15:76140400-76166000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:76140600-76153000	Weak transcription	Fetal Brain Female	brain
37	chr15:76140600-76165600	Weak transcription	Fetal Brain Male	brain
38	chr15:76141200-76154400	Weak transcription	Fetal Lung	lung
39	chr15:76141400-76195200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr15:76141600-76154200	Weak transcription	Fetal Heart	heart
41	chr15:76141600-76161800	Weak transcription	Brain Germinal Matrix	brain
42	chr15:76141600-76166000	Weak transcription	NHLF	lung
43	chr15:76142000-76154000	Weak transcription	HSMMtube	muscle
44	chr15:76142000-76161800	Weak transcription	Ovary	ovary
45	chr15:76142800-76153000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:76144600-76153000	Weak transcription	Left Ventricle	heart
47	chr15:76144800-76165800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr15:76145000-76151400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr15:76145200-76195200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr15:76145600-76161600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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