Variant report

Variant	rs4886992
Chromosome Location	chr15:78325229-78325230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78324962..78326777-chr15:78328172..78330506,2	K562	blood:
2	chr15:78324279..78326557-chr15:78328484..78331455,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221476	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10444863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10519181	1.00[ASW][hapmap];0.84[CEU][hapmap];0.86[MEX][hapmap]
rs12593545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1442293	0.84[CEU][hapmap]
rs16969422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17477813	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs1837913	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs2044099	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs35472584	0.88[CEU][hapmap]
rs3784326	1.00[ASW][hapmap]
rs4395040	1.00[ASW][hapmap];0.86[MEX][hapmap]
rs4886989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56357772	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs872926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs894301	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4886992	IDH3A	cis	cerebellum	SCAN
rs4886992	MORF4L1	cis	parietal	SCAN
rs4886992	PSMA4	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:78301400-78342200	Weak transcription	HMEC	breast
3	chr15:78303200-78342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:78305400-78329800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:78305600-78325800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:78307200-78342000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:78308800-78327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:78309200-78330200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:78309200-78330800	Weak transcription	A549	lung
10	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:78311800-78326800	Weak transcription	K562	blood
12	chr15:78313000-78327600	Weak transcription	Fetal Brain Male	brain
13	chr15:78316000-78332400	Weak transcription	Hela-S3	cervix
14	chr15:78316200-78326200	Weak transcription	Fetal Kidney	kidney
15	chr15:78317000-78327800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:78317000-78344400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr15:78317400-78326000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:78317400-78326200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:78317400-78342600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:78317600-78326800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:78317600-78327000	Weak transcription	NH-A	brain
22	chr15:78317600-78327400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:78317800-78326400	Weak transcription	Gastric	stomach
24	chr15:78317800-78326600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:78317800-78326600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr15:78317800-78326600	Weak transcription	Spleen	Spleen
27	chr15:78317800-78331000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:78317800-78344400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:78317800-78344400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr15:78318400-78325800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:78318400-78326800	Weak transcription	HepG2	liver
32	chr15:78318800-78326600	Weak transcription	Stomach Mucosa	stomach
33	chr15:78319600-78326600	Weak transcription	Colonic Mucosa	Colon
34	chr15:78320000-78325800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr15:78320000-78326000	Weak transcription	HUVEC	blood vessel
36	chr15:78320200-78327600	Weak transcription	Fetal Brain Female	brain
37	chr15:78320200-78334400	Weak transcription	Aorta	Aorta
38	chr15:78320400-78326200	Weak transcription	Brain Substantia Nigra	brain
39	chr15:78320400-78326600	Weak transcription	Pancreas	Pancrea
40	chr15:78320400-78326800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr15:78320400-78331800	Weak transcription	Esophagus	oesophagus
42	chr15:78320600-78326600	Weak transcription	Left Ventricle	heart
43	chr15:78321000-78326600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:78321000-78326800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr15:78321200-78326600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr15:78321200-78343800	Weak transcription	NHEK	skin
47	chr15:78321400-78326600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:78321600-78327000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:78322000-78326400	Weak transcription	Fetal Stomach	stomach
50	chr15:78322000-78326600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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