Variant report

Variant	rs8024695
Chromosome Location	chr15:55639305-55639306
allele	C/T
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	POLR2A	chr15:55635337-55643349	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:55638077..55640418-chr15:55645397..55647680,2	K562	blood:
2	chr15:55637488..55639591-chr15:55641186..55643179,3	MCF-7	breast:
3	chr15:55638918..55640677-chr15:55646160..55647680,2	K562	blood:
4	chr15:55639076..55640732-chr15:55640931..55642557,2	MCF-7	breast:

Variant related genes	Relation type
PIGB	TF binding region
ENSG00000069943	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10851588	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs11071180	0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs11071181	0.86[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs11490399	0.82[ASN][1000 genomes]
rs11629613	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11635532	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11636687	0.90[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11638111	0.80[ASN][1000 genomes]
rs11639418	0.81[CHB][hapmap];0.80[CHD][hapmap]
rs11639453	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11857303	0.80[ASN][1000 genomes]
rs12050587	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12050662	0.82[ASN][1000 genomes]
rs12050663	0.82[ASN][1000 genomes]
rs2290341	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2290343	0.87[ASN][1000 genomes]
rs2290344	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2305424	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2414409	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs28636865	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28657774	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28668016	0.86[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs28680176	0.82[ASN][1000 genomes]
rs28706887	0.85[ASN][1000 genomes]
rs28748576	0.85[ASN][1000 genomes]
rs34848296	0.82[ASN][1000 genomes]
rs3743203	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4774764	0.81[ASN][1000 genomes]
rs4774766	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs55661134	0.83[ASN][1000 genomes]
rs55933611	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56257633	0.83[ASN][1000 genomes]
rs67230579	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs692062	0.81[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs7174876	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7183157	0.86[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7183960	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs72742273	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72742282	0.87[AMR][1000 genomes]
rs9920058	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9920522	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv904243	chr15:55627528-55734158	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8024695	PIGB	Cis_1M	lymphoblastoid	RTeQTL
rs8024695	PIGB	cis	lymphoblastoid	seeQTL
rs8024695	RAB27A	cis	cerebellum	SCAN
rs8024695	PRTG	cis	cerebellum	SCAN
rs8024695	RAB27A	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55640000	Weak transcription	Gastric	stomach
2	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
3	chr15:55612000-55665000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:55612000-55671000	Weak transcription	Right Ventricle	heart
5	chr15:55612000-55671000	Weak transcription	Small Intestine	intestine
6	chr15:55612600-55640400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:55612600-55650200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:55612600-55663600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:55612600-55675600	Weak transcription	Aorta	Aorta
10	chr15:55612800-55640400	Weak transcription	NHLF	lung
11	chr15:55612800-55649600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:55612800-55677600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:55614800-55649000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:55619600-55640000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:55620400-55658000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:55623000-55652600	Weak transcription	Psoas Muscle	Psoas
17	chr15:55623400-55642200	Weak transcription	Hela-S3	cervix
18	chr15:55623800-55660200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:55624000-55642800	Weak transcription	Esophagus	oesophagus
20	chr15:55624200-55640400	Weak transcription	Spleen	Spleen
21	chr15:55625200-55643000	Strong transcription	Primary T cells from cord blood	blood
22	chr15:55626000-55649600	Weak transcription	HUVEC	blood vessel
23	chr15:55628400-55639800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr15:55628600-55647800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:55629800-55640200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:55630000-55695000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr15:55630200-55649000	Weak transcription	Osteobl	bone
28	chr15:55630400-55644400	Weak transcription	A549	lung
29	chr15:55630400-55654600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr15:55630400-55675600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:55630600-55640400	Weak transcription	Thymus	Thymus
32	chr15:55630600-55648000	Weak transcription	HepG2	liver
33	chr15:55630600-55655800	Weak transcription	Brain Angular Gyrus	brain
34	chr15:55630600-55660200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr15:55630600-55663200	Weak transcription	Fetal Lung	lung
36	chr15:55630600-55667800	Weak transcription	Colon Smooth Muscle	Colon
37	chr15:55630600-55668400	Weak transcription	Brain Substantia Nigra	brain
38	chr15:55630800-55640400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr15:55630800-55647000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:55630800-55652400	Weak transcription	Fetal Muscle Leg	muscle
41	chr15:55630800-55683600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr15:55631000-55640200	Weak transcription	Lung	lung
43	chr15:55631000-55667800	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:55631200-55640200	Weak transcription	Fetal Intestine Small	intestine
45	chr15:55631200-55644600	Weak transcription	Fetal Intestine Large	intestine
46	chr15:55631200-55646600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:55631200-55663200	Weak transcription	Pancreas	Pancrea
48	chr15:55631200-55674000	Weak transcription	Placenta	Placenta
49	chr15:55631800-55649600	Weak transcription	NH-A	brain
50	chr15:55632000-55646800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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