Variant report

Variant	rs11053687
Chromosome Location	chr12:10366088-10366089
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	MXI1	chr12:10364703-10367409	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:10364739-10366590	HepG2	liver:	n/a	n/a
3	SMC3	chr12:10365864-10367815	Hela-S3	cervix:	n/a	chr12:10366921-10366928
4	STAT5A	chr12:10365815-10366660	GM12878	blood:	n/a	chr12:10365912-10365935 chr12:10365924-10365938 chr12:10366634-10366646 chr12:10365838-10365850
5	POLR2A	chr12:10365806-10366559	K562	blood:	n/a	n/a
6	SP1	chr12:10365951-10366305	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:10365870-10366518	U87	brain:	n/a	n/a
8	POLR2A	chr12:10365850-10366487	GM12891	blood:	n/a	n/a
9	MAX	chr12:10366056-10366747	A549	lung:	n/a	chr12:10366638-10366648
10	POLR2A	chr12:10364743-10368315	Hela-S3	cervix:	n/a	n/a
11	MAX	chr12:10366088-10366455	GM12878	blood:	n/a	n/a
12	MXI1	chr12:10364694-10366620	Hela-S3	cervix:	n/a	n/a
13	CREB1	chr12:10364729-10366638	GM12878	blood:	n/a	chr12:10365443-10365456
14	CHD1	chr12:10365043-10366897	H1-hESC	embryonic stem cell:	n/a	chr12:10365423-10365433
15	GTF2F1	chr12:10365926-10367906	Hela-S3	cervix:	n/a	n/a
16	ATF2	chr12:10365869-10366594	GM12878	blood:	n/a	n/a
17	BHLHE40	chr12:10366026-10366509	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:10365861-10366294	HUVEC	blood vessel:	n/a	n/a
19	ELK1	chr12:10366052-10366558	Hela-S3	cervix:	n/a	n/a
20	MAFF	chr12:10366045-10366301	HepG2	liver:	n/a	n/a
21	POLR2A	chr12:10365981-10366730	HepG2	liver:	n/a	n/a
22	MXI1	chr12:10365971-10366512	HepG2	liver:	n/a	n/a
23	BRCA1	chr12:10365994-10366533	Hela-S3	cervix:	n/a	n/a
24	TAF1	chr12:10365888-10366341	GM12878	blood:	n/a	n/a
25	TAF7	chr12:10365894-10366272	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr12:10365863-10366654	HL-60	blood:	n/a	n/a
27	TAF7	chr12:10365903-10366202	H1-hESC	embryonic stem cell:	n/a	n/a
28	HEY1	chr12:10365975-10366308	K562	blood:	n/a	n/a
29	EGR1	chr12:10364800-10366228	HCT-116	colon:	n/a	chr12:10365422-10365432 chr12:10365421-10365431 chr12:10365012-10365019 chr12:10365864-10365878
30	POLR2A	chr12:10365853-10366438	U87	brain:	n/a	n/a
31	POLR2A	chr12:10364785-10367267	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr12:10365876-10366485	U87	brain:	n/a	n/a
33	POLR2A	chr12:10364768-10367850	Hela-S3	cervix:	n/a	n/a
34	YY1	chr12:10365930-10366254	GM12878	blood:	n/a	n/a
35	PML	chr12:10365971-10366723	GM12878	blood:	n/a	n/a
36	RUNX3	chr12:10365818-10366790	GM12878	blood:	n/a	chr12:10366114-10366129
37	CEBPB	chr12:10365977-10366577	ECC-1	luminal epithelium:	n/a	n/a
38	MAX	chr12:10365883-10366696	ECC-1	luminal epithelium:	n/a	chr12:10366638-10366648
39	POLR2A	chr12:10364780-10366813	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr12:10364564-10366597	H1-hESC	embryonic stem cell:	n/a	n/a
41	SMARCB1	chr12:10364547-10366841	Hela-S3	cervix:	n/a	chr12:10364966-10364975 chr12:10366071-10366080
42	TAF1	chr12:10365944-10366197	K562	blood:	n/a	n/a
43	POLR2A	chr12:10365818-10366528	GM12891	blood:	n/a	n/a
44	TAF1	chr12:10364650-10366760	H1-hESC	embryonic stem cell:	n/a	n/a
45	FOS	chr12:10366011-10366310	MCF10A-Er-Src	breast:	n/a	chr12:10366071-10366081 chr12:10366072-10366080 chr12:10366071-10366081 chr12:10366070-10366082 chr12:10366071-10366081
46	POLR2A	chr12:10365925-10368484	K562	blood:	n/a	n/a
47	POLR2A	chr12:10364816-10366689	NB4	blood:	n/a	n/a
48	CCNT2	chr12:10365991-10366299	K562	blood:	n/a	n/a
49	POLR2A	chr12:10365907-10366369	SK-N-MC	brain:	n/a	n/a
50	POLR2A	chr12:10365811-10366504	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:10365255..10367563-chr12:11322614..11325373,2	K562	blood:
2	chr12:10363710..10369534-chr12:10376619..10381190,6	K562	blood:
3	chr12:10365073..10366945-chr12:10874439..10876168,2	K562	blood:
4	chr12:10364094..10366158-chr12:10825514..10827785,2	K562	blood:
5	chr12:9913257..9914775-chr12:10363988..10366451,2	K562	blood:
6	chr12:9913275..9915086-chr12:10364378..10366451,2	K562	blood:

Variant related genes	Relation type
GABARAPL1	TF binding region
ENSG00000256712	Chromatin interaction
ENSG00000060140	Chromatin interaction
ENSG00000110848	Chromatin interaction
ENSG00000212127	Chromatin interaction
ENSG00000134539	Chromatin interaction
ENSG00000060138	Chromatin interaction
ENSG00000256537	Chromatin interaction
ENSG00000111215	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10845072	0.81[ASN][1000 genomes]
rs11053685	0.87[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11053686	0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11053689	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12821011	0.87[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4764322	0.80[ASN][1000 genomes]
rs4764323	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4764324	0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs9300225	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[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	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1054811	chr12:10350587-10440005	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11053687	GABARAPL1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10364000-10367400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:10364200-10367600	Active TSS	HSMMtube	muscle
3	chr12:10364400-10366600	Active TSS	A549	lung
4	chr12:10364400-10368200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:10364600-10366200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:10364600-10366200	Active TSS	Fetal Muscle Leg	muscle
7	chr12:10364600-10366200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr12:10364600-10366200	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr12:10364600-10366400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:10364600-10366400	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr12:10364600-10366600	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr12:10364600-10366800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:10364600-10366800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:10364600-10366800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:10364600-10366800	Active TSS	Brain Anterior Caudate	brain
16	chr12:10364600-10366800	Active TSS	Fetal Lung	lung
17	chr12:10364600-10367000	Active TSS	Brain Substantia Nigra	brain
18	chr12:10364600-10367000	Active TSS	Stomach Smooth Muscle	stomach
19	chr12:10364600-10367200	Active TSS	Liver	Liver
20	chr12:10364600-10367200	Active TSS	Rectal Smooth Muscle	rectum
21	chr12:10364600-10367400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr12:10364600-10367400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr12:10364600-10367400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:10364600-10367400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:10364600-10367400	Active TSS	Brain Cingulate Gyrus	brain
26	chr12:10364600-10367400	Active TSS	Thymus	Thymus
27	chr12:10364600-10367600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr12:10364600-10367600	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr12:10364600-10367600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:10364600-10367600	Active TSS	Brain Angular Gyrus	brain
31	chr12:10364600-10367600	Active TSS	Fetal Brain Female	brain
32	chr12:10364600-10367600	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr12:10364600-10367600	Active TSS	K562	blood
34	chr12:10364600-10367600	Active TSS	Osteobl	bone
35	chr12:10364600-10367800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:10364600-10367800	Active TSS	Colon Smooth Muscle	Colon
37	chr12:10364600-10368000	Active TSS	HSMM	muscle
38	chr12:10364600-10368200	Active TSS	Colonic Mucosa	Colon
39	chr12:10364600-10368400	Active TSS	Fetal Kidney	kidney
40	chr12:10364600-10368800	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr12:10364800-10366200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:10364800-10366400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:10364800-10366400	Active TSS	Monocytes-CD14+_RO01746	blood
44	chr12:10364800-10366600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr12:10364800-10366600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr12:10364800-10366600	Active TSS	Fetal Intestine Large	intestine
47	chr12:10364800-10366600	Active TSS	Fetal Stomach	stomach
48	chr12:10364800-10366800	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr12:10364800-10366800	Active TSS	Muscle Satellite Cultured Cells	--
50	chr12:10364800-10366800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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