Variant report

Variant	rs7176022
Chromosome Location	chr15:75107880-75107881
allele	A/C
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	EP300	chr15:75107255-75108063	SK-N-SH	brain:	n/a	chr15:75107620-75107630 chr15:75107742-75107758
2	SPI1	chr15:75107827-75108334	HL-60	blood:	n/a	n/a
3	RCOR1	chr15:75107613-75108191	Hela-S3	cervix:	n/a	n/a
4	NFIC	chr15:75107402-75107922	ECC-1	luminal epithelium:	n/a	n/a
5	SPI1	chr15:75107834-75108168	GM12891	blood:	n/a	n/a
6	SPI1	chr15:75107849-75108212	HL-60	blood:	n/a	n/a
7	SPI1	chr15:75107853-75108282	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75074156..75079604-chr15:75107384..75112501,9	MCF-7	breast:
2	chr15:75090919..75095080-chr15:75105772..75108722,6	MCF-7	breast:
3	chr15:75106165..75113668-chr15:75132311..75136608,10	MCF-7	breast:
4	chr15:75080218..75087203-chr15:75106250..75113071,13	MCF-7	breast:
5	chr15:75105168..75109047-chr15:75134120..75137766,4	K562	blood:

Variant related genes	Relation type
ENSG00000261606	TF binding region
LMAN1L	TF binding region
ENSG00000140474	Chromatin interaction
ENSG00000264386	Chromatin interaction
ENSG00000103653	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs11072509	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12441505	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12442901	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1350193	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1378938	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543927	0.91[CEU][hapmap]
rs1869959	0.86[CEU][hapmap]
rs2071501	0.84[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2168519	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2301249	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784790	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3935077	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886406	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs4886615	0.83[CEU][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap]
rs4886619	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]
rs4886629	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[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];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162232	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7180484	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72625792	0.84[ASN][1000 genomes]
rs72730503	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7497201	0.83[GIH][hapmap]
rs8031937	0.83[GIH][hapmap]
rs8033381	0.87[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8042694	0.83[GIH][hapmap]
rs9210	0.91[CEU][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap]
rs936226	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs936228	0.82[CEU][hapmap];0.90[GIH][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs936229	0.82[CEU][hapmap];0.90[GIH][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs936230	0.87[CEU][hapmap];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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7176022	NEO1	cis	parietal	SCAN
rs7176022	SCAMP2	cis	parietal	SCAN
rs7176022	ULK3	cis	Whole Blood	GTEx
rs7176022	SCAMP5	cis	cerebellum	SCAN
rs7176022	MPI	cis	parietal	SCAN
rs7176022	ULK3	cis	multi-tissue	Pritchard
rs7176022	MPI	cis	multi-tissue	Pritchard
rs7176022	MPI	cis	lymphoblastoid	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75096000-75109000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr15:75096200-75109600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:75096800-75109000	Weak transcription	Fetal Intestine Large	intestine
4	chr15:75096800-75109200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:75096800-75109400	Weak transcription	HUVEC	blood vessel
6	chr15:75096800-75109800	Weak transcription	NH-A	brain
7	chr15:75097000-75109200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:75097000-75109400	Weak transcription	Brain Anterior Caudate	brain
9	chr15:75097200-75108000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr15:75097200-75109400	Weak transcription	Lung	lung
11	chr15:75097600-75108600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:75097600-75111000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:75097800-75109200	Weak transcription	Brain Germinal Matrix	brain
14	chr15:75101200-75109000	Weak transcription	HMEC	breast
15	chr15:75101800-75109200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:75101800-75113200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:75102000-75108800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr15:75102600-75109600	Weak transcription	NHLF	lung
19	chr15:75105400-75108600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:75107000-75108600	Enhancers	Hela-S3	cervix
21	chr15:75107000-75112200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr15:75107200-75108000	Enhancers	Liver	Liver
23	chr15:75107200-75108000	Enhancers	Duodenum Mucosa	Duodenum
24	chr15:75107200-75108000	Enhancers	Pancreas	Pancrea
25	chr15:75107200-75108000	Enhancers	Right Atrium	heart
26	chr15:75107200-75108000	Enhancers	Stomach Smooth Muscle	stomach
27	chr15:75107200-75108200	Enhancers	Fetal Heart	heart
28	chr15:75107200-75108200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr15:75107200-75108200	Enhancers	Stomach Mucosa	stomach
30	chr15:75107200-75108400	Enhancers	Gastric	stomach
31	chr15:75107200-75108400	Enhancers	Rectal Smooth Muscle	rectum
32	chr15:75107200-75108400	Enhancers	Right Ventricle	heart
33	chr15:75107200-75108600	Enhancers	Spleen	Spleen
34	chr15:75107200-75108800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr15:75107200-75109000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:75107200-75109600	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr15:75107200-75110000	Enhancers	Colon Smooth Muscle	Colon
38	chr15:75107200-75111200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr15:75107200-75111400	Enhancers	Esophagus	oesophagus
40	chr15:75107200-75111800	Enhancers	Colonic Mucosa	Colon
41	chr15:75107200-75112400	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr15:75107200-75114400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:75107400-75108000	Enhancers	Placenta	Placenta
44	chr15:75107400-75108200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:75107400-75108200	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr15:75107400-75108200	Enhancers	Fetal Stomach	stomach
47	chr15:75107400-75108600	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr15:75107600-75108000	Weak transcription	HSMMtube	muscle
49	chr15:75107600-75108200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr15:75107600-75108200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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