Variant report

Variant	rs4886619
Chromosome Location	chr15:75106138-75106139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr15:75106101-75106301	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:74907274..74909845-chr15:75104512..75106785,2	MCF-7	breast:
2	chr15:75090919..75095080-chr15:75105772..75108722,6	MCF-7	breast:
3	chr15:75105168..75109047-chr15:75134120..75137766,4	K562	blood:
4	chr15:75079479..75082400-chr15:75103794..75106182,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261606	TF binding region
ENSG00000264386	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000140474	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11072509	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11634474	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12441505	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442901	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1350193	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1378938	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543927	0.91[CEU][hapmap]
rs1869959	0.81[CEU][hapmap]
rs2071501	0.84[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2168519	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2301249	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3784790	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3935077	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886406	0.91[CEU][hapmap];0.82[CHB][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap]
rs4886615	0.90[GIH][hapmap];0.86[LWK][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs4886629	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495126	0.83[GIH][hapmap]
rs6495127	0.83[GIH][hapmap]
rs7085	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7162232	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7176022	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7180484	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72625792	0.83[ASN][1000 genomes]
rs72730503	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7497201	0.83[GIH][hapmap]
rs8031937	0.83[GIH][hapmap]
rs8033381	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8042694	0.83[GIH][hapmap]
rs9210	0.82[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.82[TSI][hapmap]
rs936226	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs936228	0.90[GIH][hapmap];0.82[LWK][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs936229	0.90[GIH][hapmap];0.82[LWK][hapmap];0.82[TSI][hapmap]
rs936230	0.83[GIH][hapmap]

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	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4886619	SCAMP2	cis	parietal	SCAN
rs4886619	SCAMP5	cis	cerebellum	SCAN
rs4886619	NEO1	cis	parietal	SCAN
rs4886619	MPI	cis	parietal	SCAN
rs4886619	ULK3	cis	Whole Blood	GTEx
rs4886619	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs4886619	MPI	cis	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75086000-75107400	Weak transcription	Fetal Brain Male	brain
2	chr15:75096000-75109000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr15:75096200-75109600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:75096600-75107200	Weak transcription	Gastric	stomach
5	chr15:75096600-75107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:75096800-75107200	Weak transcription	Pancreas	Pancrea
7	chr15:75096800-75107200	Weak transcription	A549	lung
8	chr15:75096800-75107400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:75096800-75107400	Weak transcription	HSMMtube	muscle
10	chr15:75096800-75109000	Weak transcription	Fetal Intestine Large	intestine
11	chr15:75096800-75109200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:75096800-75109400	Weak transcription	HUVEC	blood vessel
13	chr15:75096800-75109800	Weak transcription	NH-A	brain
14	chr15:75097000-75107200	Weak transcription	Spleen	Spleen
15	chr15:75097000-75107600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:75097000-75109200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:75097000-75109400	Weak transcription	Brain Anterior Caudate	brain
18	chr15:75097200-75108000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr15:75097200-75109400	Weak transcription	Lung	lung
20	chr15:75097600-75108600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:75097600-75111000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:75097800-75107800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:75097800-75109200	Weak transcription	Brain Germinal Matrix	brain
24	chr15:75100800-75107800	Weak transcription	GM12878-XiMat	blood
25	chr15:75101200-75107200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:75101200-75109000	Weak transcription	HMEC	breast
27	chr15:75101800-75107200	Weak transcription	Colonic Mucosa	Colon
28	chr15:75101800-75107200	Weak transcription	Esophagus	oesophagus
29	chr15:75101800-75109200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr15:75101800-75113200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr15:75102000-75107400	Weak transcription	Placenta	Placenta
32	chr15:75102000-75108800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr15:75102400-75107600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:75102600-75109600	Weak transcription	NHLF	lung
35	chr15:75105400-75107200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:75105400-75107200	Weak transcription	Left Ventricle	heart
37	chr15:75105400-75107400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:75105400-75108600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:75105600-75106600	Enhancers	Hela-S3	cervix
40	chr15:75105600-75107200	Weak transcription	Fetal Lung	lung
41	chr15:75105600-75107400	Weak transcription	Fetal Stomach	stomach
42	chr15:75105800-75107200	Weak transcription	Right Atrium	heart
43	chr15:75105800-75107200	Weak transcription	Right Ventricle	heart
44	chr15:75105800-75107400	Weak transcription	Brain Inferior Temporal Lobe	brain

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