Variant report

Variant	rs13377622
Chromosome Location	chr12:49464221-49464222
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	chr12:49463172-49464289	GM12892	blood:	n/a	n/a
2	RELA	chr12:49463334-49464261	GM18951	blood:	n/a	n/a
3	EP300	chr12:49463295-49464228	K562	blood:	n/a	chr12:49463947-49463961
4	MAX	chr12:49463158-49464306	A549	lung:	n/a	n/a
5	MAX	chr12:49463173-49464378	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr12:49463303-49464321	PBDE	blood:	n/a	n/a
7	SP1	chr12:49463219-49464224	A549	lung:	n/a	chr12:49463810-49463819 chr12:49463811-49463820 chr12:49463809-49463821 chr12:49463242-49463256 chr12:49463242-49463252 chr12:49463575-49463584 chr12:49464149-49464163 chr12:49463821-49463842 chr12:49463810-49463824 chr12:49463809-49463821 chr12:49463809-49463820
8	MAX	chr12:49463051-49464374	A549	lung:	n/a	n/a
9	TCF12	chr12:49463032-49464273	A549	lung:	n/a	chr12:49463094-49463104
10	FOXM1	chr12:49463319-49464400	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr12:49463454-49464228	GM12878	blood:	n/a	n/a
12	NFATC1	chr12:49463751-49464299	GM12878	blood:	n/a	n/a
13	RELA	chr12:49463467-49464384	GM19099	blood:	n/a	n/a
14	MAX	chr12:49463224-49464315	HCT-116	colon:	n/a	n/a
15	REST	chr12:49462851-49464366	H1-neurons	neurons:	n/a	chr12:49463911-49463924
16	JUND	chr12:49463183-49464481	GM12878	blood:	n/a	chr12:49463943-49463955
17	SP1	chr12:49463197-49464245	A549	lung:	n/a	chr12:49463810-49463819 chr12:49463811-49463820 chr12:49463809-49463821 chr12:49463242-49463256 chr12:49463242-49463252 chr12:49463575-49463584 chr12:49464149-49464163 chr12:49463821-49463842 chr12:49463810-49463824 chr12:49463809-49463821 chr12:49463809-49463820
18	USF1	chr12:49463229-49464242	HCT-116	colon:	n/a	chr12:49463716-49463732 chr12:49463801-49463817 chr12:49463857-49463873
19	TAF1	chr12:49463651-49464224	A549	lung:	n/a	n/a
20	POLR2A	chr12:49463416-49464275	HepG2	liver:	n/a	n/a
21	IRF1	chr12:49463412-49464366	K562	blood:	n/a	chr12:49463699-49463713 chr12:49463952-49463962 chr12:49463694-49463714 chr12:49463698-49463712 chr12:49463948-49463962 chr12:49463807-49463821
22	RCOR1	chr12:49463282-49464279	Hela-S3	cervix:	n/a	n/a
23	POU2F2	chr12:49463308-49464242	GM12878	blood:	n/a	n/a
24	TEAD4	chr12:49463145-49464329	K562	blood:	n/a	n/a
25	POLR2A	chr12:49463306-49464408	GM12878	blood:	n/a	n/a
26	JUN	chr12:49462658-49464482	K562	blood:	n/a	chr12:49463943-49463955
27	MAX	chr12:49463183-49464303	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr12:49463075-49464517	PFSK-1	brain:	n/a	n/a
29	STAT5A	chr12:49463404-49464280	GM12878	blood:	n/a	chr12:49463429-49463437
30	MXI1	chr12:49463302-49464371	Hela-S3	cervix:	n/a	chr12:49463734-49463743
31	POLR2A	chr12:49463350-49464255	GM12878	blood:	n/a	n/a
32	MAFK	chr12:49463304-49464231	Hela-S3	cervix:	n/a	chr12:49463872-49463887
33	RUNX3	chr12:49463106-49464305	GM12878	blood:	n/a	chr12:49464044-49464053 chr12:49464044-49464053 chr12:49464045-49464060
34	RELA	chr12:49463271-49464349	GM15510	blood:	n/a	n/a
35	POLR2A	chr12:49463323-49464330	GM12891	blood:	n/a	n/a
36	BHLHE40	chr12:49463373-49464272	GM12878	blood:	n/a	chr12:49463716-49463732 chr12:49463801-49463817 chr12:49463857-49463873
37	MAX	chr12:49463211-49464291	GM12878	blood:	n/a	n/a
38	TBP	chr12:49463503-49464323	Hela-S3	cervix:	n/a	n/a
39	NRF1	chr12:49462832-49464358	SK-N-SH	brain:	n/a	chr12:49463636-49463650 chr12:49463916-49463930 chr12:49463916-49463927 chr12:49463918-49463927 chr12:49463913-49463927 chr12:49463916-49463927
40	MTA3	chr12:49462900-49464527	GM12878	blood:	n/a	n/a
41	MAX	chr12:49463263-49464305	SK-N-SH	brain:	n/a	n/a
42	NFIC	chr12:49463691-49464280	GM12878	blood:	n/a	n/a
43	MAX	chr12:49463343-49464349	NB4	blood:	n/a	n/a
44	POLR2A	chr12:49463211-49464364	PFSK-1	brain:	n/a	n/a
45	POLR2A	chr12:49463132-49464263	K562	blood:	n/a	n/a
46	PML	chr12:49463196-49464332	GM12878	blood:	n/a	n/a
47	TBP	chr12:49463349-49464380	GM12878	blood:	n/a	n/a
48	SMARCC2	chr12:49463058-49464223	Hela-S3	cervix:	n/a	n/a
49	MXI1	chr12:49463194-49464399	IMR90	lung:	n/a	chr12:49463203-49463218 chr12:49463734-49463743
50	NR2F2	chr12:49463204-49464540	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49446392..49469923-chr12:49518127..49527853,66	K562	blood:
2	chr12:49462406..49465445-chr12:49657502..49661212,4	K562	blood:
3	chr12:49462171..49464996-chr12:49523872..49525977,3	MCF-7	breast:
4	chr12:49452319..49453848-chr12:49464029..49465894,2	MCF-7	breast:
5	chr12:49462517..49467862-chr12:49502773..49505660,4	MCF-7	breast:
6	chr12:49451508..49465481-chr12:49521303..49528986,40	MCF-7	breast:
7	chr12:49410463..49414527-chr12:49462417..49465664,5	K562	blood:
8	chr12:49440399..49469923-chr12:49518291..49528303,83	K562	blood:
9	chr12:49462240..49465825-chr12:49663317..49667869,4	K562	blood:
10	chr12:49460491..49475559-chr12:49480736..49489831,23	K562	blood:

Variant related genes	Relation type
RHEBL1	TF binding region
ENSG00000167553	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000139549	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000200309	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12303646	0.86[AFR][1000 genomes]
rs12304391	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12309341	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs12310024	0.85[AFR][1000 genomes]
rs12315734	0.82[ASW][hapmap]
rs13377924	0.96[AFR][1000 genomes]
rs13377927	0.96[AFR][1000 genomes]
rs4018512	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13377622	TUBA1A	cis	lymphoblastoid	seeQTL
rs13377622	PRKAG1	cis	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49462800-49464400	Flanking Active TSS	Liver	Liver
2	chr12:49462800-49464400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:49463000-49464400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr12:49463000-49464400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr12:49463200-49464400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:49463200-49464400	Active TSS	Right Atrium	heart
7	chr12:49463400-49464400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:49463400-49464400	Active TSS	Brain Germinal Matrix	brain
9	chr12:49463400-49464400	Active TSS	Psoas Muscle	Psoas
10	chr12:49463400-49464600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:49463600-49464400	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr12:49463600-49464400	Active TSS	NH-A	brain
13	chr12:49463800-49464400	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr12:49464000-49464400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr12:49464000-49464400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:49464000-49464400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:49464000-49464400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:49464000-49464400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr12:49464000-49464400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:49464000-49464400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
21	chr12:49464000-49464400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
22	chr12:49464000-49464400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
23	chr12:49464000-49464400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:49464000-49464400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:49464000-49464400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr12:49464000-49464400	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr12:49464000-49464400	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr12:49464000-49464400	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr12:49464000-49464400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr12:49464000-49464400	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr12:49464000-49464400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr12:49464000-49464400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr12:49464000-49464400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr12:49464000-49464400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr12:49464000-49464400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:49464000-49464400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr12:49464000-49464400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr12:49464000-49464400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:49464000-49464400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:49464000-49464400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr12:49464000-49464400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:49464000-49464400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:49464000-49464400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr12:49464000-49464400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr12:49464000-49464400	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr12:49464000-49464400	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr12:49464000-49464400	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr12:49464000-49464400	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr12:49464000-49464400	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr12:49464000-49464400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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