Variant report

Variant	rs2231462
Chromosome Location	chr12:56123365-56123366
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	USF1	chr12:56122651-56123609	HCT-116	colon:	n/a	chr12:56122964-56122975 chr12:56122905-56122921 chr12:56122887-56122898
2	EP300	chr12:56122803-56123425	GM12878	blood:	n/a	chr12:56123164-56123180
3	PML	chr12:56122580-56123625	MCF-7	breast:	n/a	n/a
4	SPI1	chr12:56123330-56123532	K562	blood:	n/a	n/a
5	POLR2A	chr12:56122268-56123777	MCF10A-Er-Src	breast:	n/a	n/a
6	EGR1	chr12:56121999-56123801	HCT-116	colon:	n/a	chr12:56122149-56122159 chr12:56122310-56122323 chr12:56122996-56123006 chr12:56122996-56123005 chr12:56122992-56123006 chr12:56122313-56122323 chr12:56122532-56122542 chr12:56122995-56123008 chr12:56122994-56123009 chr12:56122344-56122354 chr12:56122995-56123008 chr12:56122995-56123008 chr12:56122996-56123007 chr12:56123533-56123547
7	POLR2A	chr12:56122519-56124246	GM12878	blood:	n/a	n/a
8	MAX	chr12:56122697-56124341	SK-N-SH	brain:	n/a	chr12:56122966-56122975 chr12:56122888-56122897 chr12:56122966-56122976 chr12:56122964-56122977 chr12:56122965-56122976 chr12:56122724-56122734 chr12:56122964-56122977 chr12:56122965-56122975 chr12:56122965-56122975 chr12:56122965-56122976 chr12:56122964-56122977 chr12:56122966-56122976 chr12:56122965-56122976
9	POLR2A	chr12:56122512-56123874	MCF-7	breast:	n/a	n/a
10	MXI1	chr12:56122829-56123592	K562	blood:	n/a	chr12:56122967-56122976 chr12:56122965-56122974 chr12:56122967-56122976 chr12:56122965-56122974
11	POLR2A	chr12:56123254-56123755	HUVEC	blood vessel:	n/a	n/a
12	NR2F2	chr12:56122827-56123656	K562	blood:	n/a	n/a
13	POLR2A	chr12:56122551-56123691	A549	lung:	n/a	n/a
14	CREB1	chr12:56122634-56123782	K562	blood:	n/a	n/a
15	REST	chr12:56123087-56124510	H1-neurons	neurons:	n/a	chr12:56123753-56123761 chr12:56124288-56124297 chr12:56124307-56124325
16	CHD2	chr12:56122688-56124003	GM12878	blood:	n/a	n/a
17	REST	chr12:56122963-56123530	A549	lung:	n/a	n/a
18	POLR2A	chr12:56121103-56124569	IMR90	lung:	n/a	n/a
19	MAZ	chr12:56122093-56124163	GM12878	blood:	n/a	chr12:56122244-56122254 chr12:56122966-56122975 chr12:56122888-56122897 chr12:56122966-56122976 chr12:56122964-56122977 chr12:56122965-56122976 chr12:56122724-56122734 chr12:56122964-56122977 chr12:56122965-56122975 chr12:56122965-56122975 chr12:56122965-56122976 chr12:56122964-56122977 chr12:56122346-56122356 chr12:56122966-56122976 chr12:56122150-56122160 chr12:56122965-56122976
20	YY1	chr12:56122851-56123404	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr12:56113532-56124497	U87	brain:	n/a	n/a
22	POLR2A	chr12:56122520-56124060	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr12:56122556-56123796	SK-N-SH	brain:	n/a	n/a
24	MAX	chr12:56122757-56123664	HUVEC	blood vessel:	n/a	chr12:56122966-56122975 chr12:56122888-56122897 chr12:56122966-56122976 chr12:56122964-56122977 chr12:56122965-56122976 chr12:56122964-56122977 chr12:56122965-56122975 chr12:56122965-56122975 chr12:56122965-56122976 chr12:56122964-56122977 chr12:56122966-56122976 chr12:56122965-56122976
25	TBP	chr12:56122892-56123744	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr12:56122568-56123920	GM12891	blood:	n/a	n/a
27	POLR2A	chr12:56122948-56123748	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr12:56122608-56123972	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:56121349-56124018	K562	blood:	n/a	n/a
30	CHD1	chr12:56120323-56124349	IMR90	lung:	n/a	n/a
31	TAF1	chr12:56122529-56123725	K562	blood:	n/a	n/a
32	POLR2A	chr12:56121588-56123832	Hela-S3	cervix:	n/a	n/a
33	PML	chr12:56122560-56123684	MCF-7	breast:	n/a	n/a
34	YY1	chr12:56123325-56123678	K562	blood:	n/a	n/a
35	HEY1	chr12:56122534-56123730	HepG2	liver:	n/a	chr12:56122773-56122788 chr12:56123092-56123107
36	SIN3A	chr12:56121558-56124313	H1-hESC	embryonic stem cell:	n/a	chr12:56122139-56122150 chr12:56122965-56122974 chr12:56123576-56123584 chr12:56122967-56122976 chr12:56122342-56122353
37	POLR2A	chr12:56122579-56123811	H1-hESC	embryonic stem cell:	n/a	n/a
38	YY1	chr12:56123223-56123694	SK-N-SH_RA	brain:	n/a	n/a
39	ELF1	chr12:56121328-56124343	GM12878	blood:	n/a	chr12:56122496-56122508 chr12:56122347-56122359 chr12:56121537-56121548 chr12:56122768-56122780 chr12:56122979-56122990
40	STAT3	chr12:56122859-56123661	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr12:56122663-56123818	GM12878	blood:	n/a	n/a
42	POLR2A	chr12:56122253-56124272	PFSK-1	brain:	n/a	n/a
43	EBF1	chr12:56122822-56123788	GM12878	blood:	n/a	n/a
44	ZNF263	chr12:56123024-56123738	HEK293-T-REx	kidney:	n/a	chr12:56123465-56123474
45	PML	chr12:56122472-56124145	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:56122522-56123698	K562	blood:	n/a	n/a
47	CBX3	chr12:56122815-56123909	K562	blood:	n/a	n/a
48	SMARCB1	chr12:56121492-56123851	Hela-S3	cervix:	n/a	chr12:56122915-56122924
49	IRF1	chr12:56122684-56123672	K562	blood:	n/a	chr12:56123522-56123536
50	USF1	chr12:56122521-56123775	HCT-116	colon:	n/a	chr12:56122964-56122975 chr12:56122905-56122921 chr12:56122887-56122898

No.	Distal block	Cell Line	Cell type
1	chr12:49760432..49761123-chr12:56123061..56123918,2	Hela-S3	cervix:
2	chr12:56122088..56125310-chr12:56509016..56512267,4	MCF-7	breast:
3	chr12:56122663..56123436-chr20:56963760..56964515,2	NB4	blood:
4	chr12:56122770..56125786-chr12:56400050..56403264,3	K562	blood:
5	chr12:56122956..56123516-chr2:201677148..201678135,2	Hela-S3	cervix:
6	chr12:56109904..56110634-chr12:56122400..56123493,3	Hela-S3	cervix:
7	chr12:56123107..56123678-chr17:73775340..73775880,2	Hela-S3	cervix:
8	chr12:56119665..56125098-chr12:56220794..56225708,11	MCF-7	breast:
9	chr12:56122473..56123456-chr12:120730401..120731352,2	Hela-S3	cervix:
10	chr1:156182629..156183186-chr12:56122790..56123462,2	Hela-S3	cervix:
11	chr12:56121779..56124068-chr12:56319367..56323030,5	K562	blood:
12	chr12:56123120..56123867-chr12:104234782..104235765,2	Hela-S3	cervix:
13	chr12:56120093..56124486-chr12:56434488..56437037,3	K562	blood:
14	chr12:56122789..56124369-chr12:56333771..56335626,2	K562	blood:
15	chr12:56121335..56123958-chr12:56496918..56499786,2	K562	blood:
16	chr12:56120851..56123825-chr12:56659216..56662167,3	K562	blood:
17	chr12:56117197..56125255-chr12:56135299..56142277,21	K562	blood:
18	chr12:56121796..56124636-chr12:56320580..56323901,5	MCF-7	breast:
19	chr12:56098994..56103683-chr12:56119699..56126107,8	MCF-7	breast:
20	chr12:56120734..56123554-chr12:56508983..56512643,4	K562	blood:
21	chr12:56122193..56124805-chr12:56319367..56323067,7	K562	blood:
22	chr12:56122056..56124298-chr12:56209901..56211592,3	MCF-7	breast:
23	chr12:56074143..56076540-chr12:56121933..56124293,2	MCF-7	breast:
24	chr12:56120240..56124369-chr12:56508983..56513755,7	K562	blood:
25	chr12:56122006..56124318-chr12:56366555..56368429,2	MCF-7	breast:
26	chr12:56120533..56123958-chr12:56496918..56499602,3	K562	blood:
27	chr12:56122035..56125892-chr12:56210581..56213887,4	K562	blood:
28	chr12:56119392..56124555-chr12:56134719..56139155,10	MCF-7	breast:
29	chr12:56118873..56123597-chr12:56135421..56141775,11	K562	blood:
30	chr12:56074050..56076493-chr12:56123343..56125140,3	MCF-7	breast:
31	chr12:56120972..56124195-chr12:56135682..56138639,8	MCF-7	breast:
32	chr12:56123089..56123589-chr17:80415974..80416712,3	HCT-116	colon:
33	chr1:86046432..86047170-chr12:56122507..56123451,2	Hela-S3	cervix:
34	chr12:56122869..56125030-chr12:56332847..56335271,2	K562	blood:
35	chr12:56120587..56125243-chr12:56320195..56323478,6	MCF-7	breast:
36	chr12:56099553..56102772-chr12:56120884..56124385,4	K562	blood:
37	chr12:56121691..56123442-chr12:56362303..56365050,2	MCF-7	breast:
38	chr12:56119294..56126638-chr12:56434111..56441706,13	K562	blood:
39	chr12:56121599..56124065-chr12:56209598..56212420,4	MCF-7	breast:
40	chr12:56123003..56123644-chr9:34651602..34652337,2	HCT-116	colon:

Variant related genes	Relation type
CD63	TF binding region
ENSG00000258311	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000170439	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000257327	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000160783	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000124164	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000082153	Chromatin interaction
ENSG00000141562	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000137070	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000132475	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000135424	Chromatin interaction
ENSG00000265458	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000135441	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000260238	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11613875	1.00[YRI][hapmap]
rs13193	0.91[EUR][1000 genomes]
rs1384604	1.00[ASW][hapmap]
rs1463591	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2231464	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3138140	0.82[TSI][hapmap]
rs4457792	0.82[CEU][hapmap]
rs58599597	0.88[EUR][1000 genomes]
rs59980563	0.82[EUR][1000 genomes]
rs73119231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7959622	1.00[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525231	chr12:56076919-56124332	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	esv3406101	chr12:56121510-56124058	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2231462	BLOC1S1	cis	lymphoblastoid	seeQTL
rs2231462	RDH5	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56121000-56123600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:56121000-56124000	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr12:56121000-56124200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:56121200-56123600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:56121200-56123800	Active TSS	Sigmoid Colon	Sigmoid Colon
6	chr12:56121200-56124000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr12:56121200-56124000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:56121200-56124000	Active TSS	Aorta	Aorta
9	chr12:56121200-56124000	Active TSS	Ovary	ovary
10	chr12:56121200-56124200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:56121200-56124200	Active TSS	HSMMtube	muscle
12	chr12:56121200-56124400	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr12:56121200-56124400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr12:56121200-56125200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:56121400-56123600	Active TSS	Fetal Intestine Large	intestine
16	chr12:56121400-56123800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:56121400-56123800	Active TSS	Psoas Muscle	Psoas
18	chr12:56121400-56123800	Active TSS	NHDF-Ad	bronchial
19	chr12:56121400-56124000	Active TSS	Gastric	stomach
20	chr12:56121400-56124200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr12:56121400-56124400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:56121600-56123400	Active TSS	GM12878-XiMat	blood
23	chr12:56121600-56123600	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr12:56121600-56123600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:56121600-56123600	Active TSS	Pancreas	Pancrea
26	chr12:56121600-56123600	Active TSS	Thymus	Thymus
27	chr12:56121600-56123600	Active TSS	A549	lung
28	chr12:56121600-56123800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:56121600-56123800	Active TSS	Small Intestine	intestine
30	chr12:56121600-56124000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:56121600-56124000	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr12:56121600-56124000	Active TSS	Lung	lung
33	chr12:56121600-56124000	Active TSS	Osteobl	bone
34	chr12:56121600-56124200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr12:56121600-56124200	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr12:56121600-56124200	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr12:56121600-56124200	Active TSS	Fetal Kidney	kidney
38	chr12:56121600-56124400	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr12:56121800-56123400	Active TSS	Stomach Mucosa	stomach
40	chr12:56121800-56123400	Active TSS	HepG2	liver
41	chr12:56121800-56123600	Active TSS	H1 Cell Line	embryonic stem cell
42	chr12:56121800-56123600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:56121800-56123600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:56121800-56123600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:56121800-56123600	Active TSS	Brain Angular Gyrus	brain
46	chr12:56121800-56123800	Active TSS	Brain Hippocampus Middle	brain
47	chr12:56121800-56124000	Active TSS	Placenta Amnion	Placenta Amnion
48	chr12:56121800-56124200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:56121800-56124200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:56121800-56124200	Active TSS	Colon Smooth Muscle	Colon

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