Variant report

Variant	rs4886747
Chromosome Location	chr15:76151081-76151082
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: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12910576	0.81[AMR][1000 genomes]
rs1391894	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1695378	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699263	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs189197	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1976748	0.88[YRI][hapmap]
rs2255701	0.81[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];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2441929	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2455899	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460798	0.87[CEU][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2460800	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2469039	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes]
rs2593277	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2593278	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2593280	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]
rs28876229	0.86[AMR][1000 genomes]
rs334930	0.81[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.96[TSI][hapmap]
rs335681	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs335697	0.81[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];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs335706	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs335711	0.81[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];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886753	0.81[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes]
rs4886754	0.83[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes]
rs71403522	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8024155	0.86[AMR][1000 genomes]
rs985849	0.81[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4886747	HIGD2B	cis	parietal	SCAN
rs4886747	NRG4	cis	cerebellum	SCAN
rs4886747	CSK	cis	parietal	SCAN
rs4886747	LRRC49	cis	cerebellum	SCAN
rs4886747	ODF3L1	cis	parietal	SCAN
rs4886747	NRG4	cis	parietal	SCAN
rs4886747	C15orf59	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	chr15:76138000-76179600	Weak transcription	Small Intestine	intestine
9	chr15:76138200-76153600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:76138200-76154000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:76138200-76154200	Weak transcription	Gastric	stomach
12	chr15:76138200-76154200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:76138200-76154200	Weak transcription	Right Atrium	heart
14	chr15:76138200-76161800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:76138200-76166000	Weak transcription	Aorta	Aorta
16	chr15:76138200-76166000	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:76138200-76166000	Weak transcription	Pancreas	Pancrea
18	chr15:76138200-76166000	Weak transcription	Spleen	Spleen
19	chr15:76138200-76183000	Weak transcription	Hela-S3	cervix
20	chr15:76138200-76195200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:76138200-76195400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:76138400-76153000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:76138400-76153000	Weak transcription	Thymus	Thymus
24	chr15:76138400-76155000	Weak transcription	NH-A	brain
25	chr15:76138400-76184000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:76138800-76166000	Weak transcription	Esophagus	oesophagus
27	chr15:76138800-76169200	Weak transcription	Psoas Muscle	Psoas
28	chr15:76139400-76152400	Weak transcription	NHDF-Ad	bronchial
29	chr15:76139400-76153200	Weak transcription	Placenta	Placenta
30	chr15:76140000-76156600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:76140000-76161800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr15:76140000-76165800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:76140000-76184000	Weak transcription	Fetal Kidney	kidney
34	chr15:76140400-76166000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:76140600-76153000	Weak transcription	Fetal Brain Female	brain
36	chr15:76140600-76165600	Weak transcription	Fetal Brain Male	brain
37	chr15:76141200-76154400	Weak transcription	Fetal Lung	lung
38	chr15:76141400-76195200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr15:76141600-76154200	Weak transcription	Fetal Heart	heart
40	chr15:76141600-76161800	Weak transcription	Brain Germinal Matrix	brain
41	chr15:76141600-76166000	Weak transcription	NHLF	lung
42	chr15:76142000-76154000	Weak transcription	HSMMtube	muscle
43	chr15:76142000-76161800	Weak transcription	Ovary	ovary
44	chr15:76142800-76153000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:76144600-76153000	Weak transcription	Left Ventricle	heart
46	chr15:76144800-76165800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr15:76145000-76151400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr15:76145200-76195200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr15:76145600-76161600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:76146000-76157800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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