Variant report

Variant	rs2138250
Chromosome Location	chr12:121122550-121122551
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	CEBPB	chr12:121122310-121122591	Hela-S3	cervix:	n/a	chr12:121122437-121122448
2	MTA3	chr12:121122092-121123176	GM12878	blood:	n/a	n/a
3	MTA3	chr12:121122204-121123092	GM12878	blood:	n/a	n/a
4	ARID3A	chr12:121122312-121122554	HepG2	liver:	n/a	n/a
5	RELA	chr12:121122431-121123237	GM15510	blood:	n/a	n/a
6	CEBPB	chr12:121122129-121123215	GM12878	blood:	n/a	chr12:121122437-121122448
7	RUNX3	chr12:121122227-121123266	GM12878	blood:	n/a	n/a
8	POU2F2	chr12:121122245-121123200	GM12878	blood:	n/a	n/a
9	BHLHE40	chr12:121122261-121123166	GM12878	blood:	n/a	n/a
10	FOXM1	chr12:121122244-121123176	GM12878	blood:	n/a	n/a
11	EP300	chr12:121122319-121123133	GM12878	blood:	n/a	chr12:121122942-121122956
12	RELA	chr12:121122287-121123174	GM19099	blood:	n/a	n/a
13	STAT3	chr12:121122293-121122576	MCF10A-Er-Src	breast:	n/a	n/a
14	RUNX3	chr12:121122252-121123310	GM12878	blood:	n/a	n/a
15	STAT5A	chr12:121122540-121123223	GM12878	blood:	n/a	chr12:121122912-121122920
16	PAX5	chr12:121122295-121122634	GM12878	blood:	n/a	n/a
17	MXI1	chr12:121122345-121123132	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:121122171-121122816	U87	brain:	n/a	n/a
19	YY1	chr12:121122458-121123044	GM12892	blood:	n/a	n/a
20	MAFK	chr12:121122228-121122584	HepG2	liver:	n/a	n/a
21	CREB1	chr12:121122060-121123256	GM12878	blood:	n/a	n/a
22	SMC3	chr12:121122398-121123135	GM12878	blood:	n/a	chr12:121122857-121122864
23	PAX5	chr12:121122178-121123172	GM12878	blood:	n/a	chr12:121122942-121122951
24	CTCF	chr12:121122539-121123080	GM12878	blood:	n/a	chr12:121122854-121122863
25	CEBPB	chr12:121122269-121122643	A549	lung:	n/a	chr12:121122437-121122448
26	TBL1XR1	chr12:121122273-121123123	GM12878	blood:	n/a	n/a
27	RCOR1	chr12:121122340-121123269	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:121122297-121123089	GM12878	blood:	n/a	n/a
29	JUND	chr12:121122245-121122561	HepG2	liver:	n/a	chr12:121122416-121122427
30	EBF1	chr12:121122274-121123570	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:121122154-121123109	GM12878	blood:	n/a	n/a
32	EP300	chr12:121122219-121123176	GM12878	blood:	n/a	chr12:121122942-121122956
33	CEBPB	chr12:121122277-121122754	HepG2	liver:	n/a	chr12:121122437-121122448
34	ATF2	chr12:121122116-121123234	GM12878	blood:	n/a	n/a
35	MYC	chr12:121122272-121122616	MCF10A-Er-Src	breast:	n/a	n/a
36	CUX1	chr12:121122426-121123116	GM12878	blood:	n/a	n/a
37	BCLAF1	chr12:121122465-121123268	GM12878	blood:	n/a	n/a
38	RELA	chr12:121122265-121123116	GM19193	blood:	n/a	n/a
39	NFIC	chr12:121122175-121123248	GM12878	blood:	n/a	n/a
40	CTCF	chr12:121122480-121122630	GM12864	blood:	n/a	n/a
41	STAT3	chr12:121122279-121123218	GM12878	blood:	n/a	chr12:121122912-121122920
42	MYC	chr12:121122293-121122740	MCF10A-Er-Src	breast:	n/a	n/a
43	CREB1	chr12:121122116-121123258	GM12878	blood:	n/a	n/a
44	BATF	chr12:121122236-121122627	GM12878	blood:	n/a	chr12:121122418-121122429
45	FOS	chr12:121122183-121122614	MCF10A-Er-Src	breast:	n/a	n/a
46	WRNIP1	chr12:121122395-121123518	GM12878	blood:	n/a	n/a
47	FOXM1	chr12:121122479-121123278	GM12878	blood:	n/a	n/a
48	PML	chr12:121122139-121123234	GM12878	blood:	n/a	chr12:121122760-121122768
49	FOS	chr12:121122199-121122618	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr12:121122300-121122968	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121095512..121100910-chr12:121122531..121126551,5	MCF-7	breast:
2	chr12:121121278..121123096-chr12:121123406..121125757,2	MCF-7	breast:
3	chr12:121110807..121113740-chr12:121121255..121124046,3	MCF-7	breast:
4	chr12:121121435..121124259-chr12:121418231..121420548,2	MCF-7	breast:
5	chr12:121122170..121123860-chr12:121162845..121164992,2	K562	blood:
6	chr12:121085923..121088804-chr12:121121977..121126483,5	MCF-7	breast:

Variant related genes	Relation type
MLEC	TF binding region
ENSG00000241388	Chromatin interaction
ENSG00000122971	Chromatin interaction
ENSG00000157782	Chromatin interaction
ENSG00000110917	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs12821493	1.00[ASN][1000 genomes]
rs2233673	1.00[ASN][1000 genomes]
rs35151295	1.00[ASN][1000 genomes]
rs35267083	1.00[ASN][1000 genomes]
rs3850521	1.00[ASN][1000 genomes]
rs3889470	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55645249	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55647329	1.00[ASN][1000 genomes]
rs55660947	1.00[ASN][1000 genomes]
rs55874815	1.00[ASN][1000 genomes]
rs55914930	1.00[ASN][1000 genomes]
rs55941696	1.00[ASN][1000 genomes]
rs55970240	1.00[ASN][1000 genomes]
rs55980956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56084677	1.00[ASN][1000 genomes]
rs56163702	1.00[ASN][1000 genomes]
rs56175661	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56178989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56183824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56189047	1.00[ASN][1000 genomes]
rs56206244	1.00[ASN][1000 genomes]
rs56231343	1.00[AFR][1000 genomes]
rs56284009	1.00[ASN][1000 genomes]
rs56366632	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56391085	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56401401	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58235352	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73213106	1.00[ASN][1000 genomes]
rs73214885	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73214888	1.00[ASN][1000 genomes]
rs73214894	1.00[ASN][1000 genomes]
rs73214896	1.00[ASN][1000 genomes]
rs73217009	1.00[ASN][1000 genomes]
rs73217017	1.00[ASN][1000 genomes]
rs73222778	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73222780	1.00[ASN][1000 genomes]
rs73222784	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73222786	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73222787	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs73222794	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73222795	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73225003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73225012	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73225023	1.00[ASN][1000 genomes]
rs73225093	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73225101	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73227016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73227022	1.00[ASN][1000 genomes]
rs73227026	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73227027	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73227029	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73227033	1.00[ASN][1000 genomes]
rs73227036	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73227038	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73229118	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73229126	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73229149	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73229151	1.00[ASN][1000 genomes]
rs73229157	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73229160	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73229162	1.00[ASN][1000 genomes]
rs73230347	1.00[ASN][1000 genomes]
rs73230349	1.00[ASN][1000 genomes]
rs73230352	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1045923	chr12:121082203-121146219	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121107400-121123400	Weak transcription	Right Atrium	heart
2	chr12:121116000-121123800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:121116000-121123800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:121116600-121123400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:121116600-121123600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:121116600-121123800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:121116600-121123800	Weak transcription	Placenta	Placenta
8	chr12:121116600-121123800	Weak transcription	Stomach Mucosa	stomach
9	chr12:121116600-121123800	Weak transcription	Osteobl	bone
10	chr12:121116800-121123600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:121116800-121123800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:121118400-121122600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:121118400-121123400	Weak transcription	Hela-S3	cervix
14	chr12:121118400-121123800	Weak transcription	Small Intestine	intestine
15	chr12:121118600-121123200	Weak transcription	Adipose Nuclei	Adipose
16	chr12:121118600-121123400	Weak transcription	HUVEC	blood vessel
17	chr12:121118600-121123800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:121118600-121123800	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:121118600-121124000	Weak transcription	Spleen	Spleen
20	chr12:121118800-121122600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:121119400-121123800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:121119600-121123800	Weak transcription	Fetal Brain Male	brain
23	chr12:121120200-121123400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:121121600-121123800	Enhancers	Primary B cells from cord blood	blood
25	chr12:121121800-121123600	Weak transcription	Fetal Intestine Large	intestine
26	chr12:121121800-121123600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:121122000-121123800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:121122000-121123800	Enhancers	Primary B cells from peripheral blood	blood
29	chr12:121122000-121123800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr12:121122200-121122600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr12:121122200-121122800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:121122200-121122800	Enhancers	A549	lung
33	chr12:121122200-121122800	Flanking Active TSS	GM12878-XiMat	blood
34	chr12:121122200-121122800	Enhancers	NHDF-Ad	bronchial
35	chr12:121122200-121122800	Enhancers	NHEK	skin
36	chr12:121122200-121123200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:121122200-121123200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:121122200-121123400	Enhancers	HepG2	liver
39	chr12:121122200-121123600	Enhancers	HMEC	breast
40	chr12:121122200-121123800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:121122200-121123800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:121122200-121123800	Weak transcription	Colonic Mucosa	Colon
43	chr12:121122400-121122600	Enhancers	Brain Hippocampus Middle	brain
44	chr12:121122400-121122800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:121122400-121123000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:121122400-121123000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:121122400-121123400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:121122400-121123600	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr12:121122400-121123800	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr12:121122400-121123800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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