Variant report

Variant	rs3138131
Chromosome Location	chr12:56122084-56122085
allele	C/G
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	NFIC	chr12:56121508-56122462	ECC-1	luminal epithelium:	n/a	n/a
2	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
3	YY1	chr12:56121946-56122413	SK-N-SH	brain:	n/a	chr12:56122026-56122040 chr12:56122345-56122354
4	ELF1	chr12:56122035-56122457	A549	lung:	n/a	chr12:56122347-56122359
5	POLR2A	chr12:56121103-56124569	IMR90	lung:	n/a	n/a
6	POLR2A	chr12:56121754-56122158	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:56113532-56124497	U87	brain:	n/a	n/a
8	ELF1	chr12:56121482-56122434	K562	blood:	n/a	chr12:56122347-56122359 chr12:56121537-56121548
9	ETS1	chr12:56121926-56122411	A549	lung:	n/a	chr12:56122345-56122356
10	MXI1	chr12:56121763-56122409	Hela-S3	cervix:	n/a	n/a
11	YY1	chr12:56121867-56122297	GM12892	blood:	n/a	chr12:56122026-56122040
12	ELF1	chr12:56121370-56122404	MCF-7	breast:	n/a	chr12:56122347-56122359 chr12:56121537-56121548
13	POLR2A	chr12:56121349-56124018	K562	blood:	n/a	n/a
14	CHD1	chr12:56120323-56124349	IMR90	lung:	n/a	n/a
15	POLR2A	chr12:56121801-56122149	GM12878	blood:	n/a	n/a
16	RUNX3	chr12:56122043-56122475	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:56121588-56123832	Hela-S3	cervix:	n/a	n/a
18	ELF1	chr12:56121925-56122399	SK-N-SH	brain:	n/a	chr12:56122347-56122359
19	CTCF	chr12:56122020-56122170	GM12870	blood:	n/a	n/a
20	SP1	chr12:56121501-56122524	A549	lung:	n/a	chr12:56122339-56122348 chr12:56122338-56122350 chr12:56122489-56122503 chr12:56122243-56122255 chr12:56122338-56122350 chr12:56122244-56122254 chr12:56122502-56122516 chr12:56122339-56122349 chr12:56122146-56122160 chr12:56122305-56122319 chr12:56121832-56121846 chr12:56122149-56122161 chr12:56122496-56122505 chr12:56122150-56122159 chr12:56122497-56122506 chr12:56122149-56122161 chr12:56122339-56122348 chr12:56122243-56122255 chr12:56122340-56122349 chr12:56122507-56122514
21	YY1	chr12:56121785-56122410	SK-N-SH_RA	brain:	n/a	chr12:56122026-56122040 chr12:56122345-56122354
22	TAF1	chr12:56121658-56122230	H1-hESC	embryonic stem cell:	n/a	n/a
23	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
24	POLR2A	chr12:56121381-56122476	Hela-S3	cervix:	n/a	n/a
25	GATA3	chr12:56121997-56122383	T-47D	breast:	n/a	n/a
26	ELF1	chr12:56121328-56124343	GM12878	blood:	n/a	chr12:56122496-56122508 chr12:56122347-56122359 chr12:56121537-56121548 chr12:56122768-56122780 chr12:56122979-56122990
27	YY1	chr12:56121979-56122252	GM12892	blood:	n/a	chr12:56122026-56122040
28	EP300	chr12:56121390-56122509	SK-N-SH	brain:	n/a	chr12:56121538-56121552
29	SMARCB1	chr12:56121492-56123851	Hela-S3	cervix:	n/a	chr12:56122915-56122924
30	YY1	chr12:56121897-56122310	SK-N-SH_RA	brain:	n/a	chr12:56122026-56122040
31	TCF12	chr12:56121319-56124183	A549	lung:	n/a	chr12:56122619-56122629
32	YY1	chr12:56121810-56122479	HepG2	liver:	n/a	chr12:56122026-56122040 chr12:56122345-56122354
33	CTCF	chr12:56121960-56122110	GM12874	blood:	n/a	n/a
34	MXI1	chr12:56121169-56124795	SK-N-SH	brain:	n/a	chr12:56122967-56122976 chr12:56122965-56122974 chr12:56122967-56122976 chr12:56122965-56122974
35	POLR2A	chr12:56121554-56123736	ECC-1	luminal epithelium:	n/a	n/a
36	CTCF	chr12:56121940-56122090	HCPEpiC	choroid plexus:	n/a	n/a
37	TAF1	chr12:56121822-56123692	ECC-1	luminal epithelium:	n/a	n/a
38	YY1	chr12:56122013-56122250	K562	blood:	n/a	chr12:56122026-56122040
39	MTA3	chr12:56121529-56122252	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:56120298-56122466	U87	brain:	n/a	n/a
41	MAX	chr12:56121668-56122571	SK-N-SH	brain:	n/a	chr12:56122244-56122254 chr12:56122346-56122356 chr12:56122150-56122160
42	MAX	chr12:56121586-56123871	HCT-116	colon:	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
43	ELF1	chr12:56122074-56122397	HepG2	liver:	n/a	chr12:56122347-56122359
44	UBTF	chr12:56121345-56123195	K562	blood:	n/a	n/a
45	CTCF	chr12:56122000-56122150	HEEpiC	esophagus:	n/a	n/a
46	POLR2A	chr12:56121518-56122114	HepG2	liver:	n/a	n/a
47	CTCF	chr12:56122000-56122150	NHEK	skin:	n/a	n/a
48	POLR2A	chr12:56121300-56122484	K562	blood:	n/a	n/a
49	POLR2A	chr12:56121482-56122171	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr12:56121940-56122090	HMEC	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56121253..56122830-chr12:56553054..56555339,2	MCF-7	breast:
2	chr12:56119665..56125098-chr12:56220794..56225708,11	MCF-7	breast:
3	chr12:56120003..56122736-chr12:56659216..56661326,3	K562	blood:
4	chr1:65886332..65886968-chr12:56121977..56122488,2	Hela-S3	cervix:
5	chr12:56121779..56124068-chr12:56319367..56323030,5	K562	blood:
6	chr12:56120093..56124486-chr12:56434488..56437037,3	K562	blood:
7	chr12:56121964..56122628-chr15:41047145..41047901,2	Hela-S3	cervix:
8	chr12:56120864..56122982-chr12:56435772..56437272,2	MCF-7	breast:
9	chr12:56120515..56122201-chr12:56332595..56334238,2	K562	blood:
10	chr12:56121335..56123958-chr12:56496918..56499786,2	K562	blood:
11	chr12:56120851..56123825-chr12:56659216..56662167,3	K562	blood:
12	chr12:56117197..56125255-chr12:56135299..56142277,21	K562	blood:
13	chr12:56121796..56124636-chr12:56320580..56323901,5	MCF-7	breast:
14	chr12:56098994..56103683-chr12:56119699..56126107,8	MCF-7	breast:
15	chr12:56121086..56122985-chr12:56327062..56330070,3	MCF-7	breast:
16	chr12:56120734..56123554-chr12:56508983..56512643,4	K562	blood:
17	chr12:56104896..56106917-chr12:56120568..56123344,2	MCF-7	breast:
18	chr12:56122056..56124298-chr12:56209901..56211592,3	MCF-7	breast:
19	chr12:56074143..56076540-chr12:56121933..56124293,2	MCF-7	breast:
20	chr12:56120240..56124369-chr12:56508983..56513755,7	K562	blood:
21	chr12:56122039..56122873-chr3:174158485..174159158,2	Hela-S3	cervix:
22	chr12:56120591..56123197-chr12:56472700..56474357,3	MCF-7	breast:
23	chr12:56122006..56124318-chr12:56366555..56368429,2	MCF-7	breast:
24	chr12:56120533..56123958-chr12:56496918..56499602,3	K562	blood:
25	chr12:56122035..56125892-chr12:56210581..56213887,4	K562	blood:
26	chr12:56119392..56124555-chr12:56134719..56139155,10	MCF-7	breast:
27	chr12:56118873..56123597-chr12:56135421..56141775,11	K562	blood:
28	chr12:56120972..56124195-chr12:56135682..56138639,8	MCF-7	breast:
29	chr12:56121261..56123274-chr12:56389263..56391155,2	K562	blood:
30	chr12:56120505..56122635-chr12:56345271..56347933,2	K562	blood:
31	chr12:56121418..56123151-chr12:56510609..56512159,2	MCF-7	breast:
32	chr12:56120587..56125243-chr12:56320195..56323478,6	MCF-7	breast:
33	chr12:56099553..56102772-chr12:56120884..56124385,4	K562	blood:
34	chr12:56121691..56123442-chr12:56362303..56365050,2	MCF-7	breast:
35	chr12:56119294..56126638-chr12:56434111..56441706,13	K562	blood:
36	chr12:56121599..56124065-chr12:56209598..56212420,4	MCF-7	breast:
37	chr12:56121284..56123165-chr12:56709581..56711185,2	K562	blood:

Variant related genes	Relation type
CD63	TF binding region
ENSG00000258056	TF binding region
ENSG00000205323	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000170439	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000213625	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000135424	Chromatin interaction
ENSG00000177694	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000116678	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000123353	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56116600-56122200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:56116800-56122200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:56117800-56122200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:56120400-56122200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
5	chr12:56120600-56122200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr12:56121000-56122200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:56121000-56122200	Flanking Active TSS	Liver	Liver
8	chr12:56121000-56123600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:56121000-56124000	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr12:56121000-56124200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:56121200-56122200	Flanking Active TSS	Fetal Thymus	thymus
12	chr12:56121200-56122400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:56121200-56123600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:56121200-56123800	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr12:56121200-56124000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr12:56121200-56124000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:56121200-56124000	Active TSS	Aorta	Aorta
18	chr12:56121200-56124000	Active TSS	Ovary	ovary
19	chr12:56121200-56124200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:56121200-56124200	Active TSS	HSMMtube	muscle
21	chr12:56121200-56124400	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr12:56121200-56124400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr12:56121200-56125200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:56121400-56122200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr12:56121400-56122200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:56121400-56122200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:56121400-56122400	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr12:56121400-56123000	Active TSS	NH-A	brain
29	chr12:56121400-56123600	Active TSS	Fetal Intestine Large	intestine
30	chr12:56121400-56123800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:56121400-56123800	Active TSS	Psoas Muscle	Psoas
32	chr12:56121400-56123800	Active TSS	NHDF-Ad	bronchial
33	chr12:56121400-56124000	Active TSS	Gastric	stomach
34	chr12:56121400-56124200	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr12:56121400-56124400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:56121600-56122200	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr12:56121600-56122200	Flanking Active TSS	Fetal Brain Male	brain
38	chr12:56121600-56122200	Flanking Active TSS	Dnd41	blood
39	chr12:56121600-56122400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr12:56121600-56122400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr12:56121600-56123200	Active TSS	HMEC	breast
42	chr12:56121600-56123400	Active TSS	GM12878-XiMat	blood
43	chr12:56121600-56123600	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr12:56121600-56123600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:56121600-56123600	Active TSS	Pancreas	Pancrea
46	chr12:56121600-56123600	Active TSS	Thymus	Thymus
47	chr12:56121600-56123600	Active TSS	A549	lung
48	chr12:56121600-56123800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:56121600-56123800	Active TSS	Small Intestine	intestine
50	chr12:56121600-56124000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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