Variant report

Variant	rs4886748
Chromosome Location	chr15:76175128-76175129
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76173887..76175756-chr15:76183628..76185544,2	K562	blood:
2	chr15:76172673..76175756-chr15:76183628..76185667,3	K562	blood:
3	chr15:76135386..76137433-chr15:76173679..76177083,4	MCF-7	breast:
4	chr15:76156695..76159097-chr15:76174173..76176640,2	K562	blood:
5	chr15:76161758..76164592-chr15:76173803..76175503,2	K562	blood:
6	chr15:76169035..76171437-chr15:76174883..76177728,2	K562	blood:
7	chr15:76168617..76171415-chr15:76174186..76176741,3	K562	blood:

Variant related genes	Relation type
ENSG00000140367	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10444856	0.96[CEU][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10851884	0.96[CEU][hapmap];0.80[GIH][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs11072562	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11072566	0.89[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs11072567	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11636251	0.92[CEU][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12437816	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12593806	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1874953	0.96[CEU][hapmap];0.83[GIH][hapmap];0.87[LWK][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1976748	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2047866	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2201917	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28525382	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28550045	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28607641	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs335685	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4886466	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4886755	0.80[ASW][hapmap];0.92[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7177266	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4886748	UBE2Q2	cis	parietal	SCAN
rs4886748	NRG4	cis	parietal	SCAN
rs4886748	NRG4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76137800-76188400	Weak transcription	Brain Anterior Caudate	brain
2	chr15:76138000-76179600	Weak transcription	Small Intestine	intestine
3	chr15:76138200-76183000	Weak transcription	Hela-S3	cervix
4	chr15:76138200-76195200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:76138200-76195400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr15:76138400-76184000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:76140000-76184000	Weak transcription	Fetal Kidney	kidney
8	chr15:76141400-76195200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:76145200-76195200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr15:76149000-76195600	Weak transcription	Colonic Mucosa	Colon
11	chr15:76152800-76193400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:76159800-76195400	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:76160800-76176000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:76161000-76182200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:76161800-76182000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:76162000-76176600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr15:76162000-76184000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr15:76164200-76177200	Strong transcription	Dnd41	blood
19	chr15:76164200-76182400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:76164400-76176800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:76164800-76176000	Weak transcription	Fetal Heart	heart
22	chr15:76165000-76178400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:76165400-76188800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:76165600-76175800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr15:76165600-76185800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:76165600-76194800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr15:76165800-76186600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:76166200-76186600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:76166400-76193600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr15:76166400-76194600	Weak transcription	Colon Smooth Muscle	Colon
31	chr15:76166400-76195200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:76166400-76195400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:76166400-76195800	Weak transcription	Gastric	stomach
34	chr15:76166600-76176000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr15:76166600-76177400	Weak transcription	Liver	Liver
36	chr15:76166600-76194400	Weak transcription	Right Ventricle	heart
37	chr15:76166600-76195200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:76166600-76195400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr15:76166600-76195800	Weak transcription	Aorta	Aorta
40	chr15:76166800-76184200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:76166800-76195400	Weak transcription	Fetal Intestine Small	intestine
42	chr15:76167000-76177000	Weak transcription	Thymus	Thymus
43	chr15:76167000-76177400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:76167000-76177600	Weak transcription	Pancreas	Pancrea
45	chr15:76167000-76194400	Weak transcription	Spleen	Spleen
46	chr15:76167000-76195600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:76167000-76195800	Weak transcription	Esophagus	oesophagus
48	chr15:76167200-76176000	Weak transcription	A549	lung
49	chr15:76167200-76182400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:76167200-76184000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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