Variant report

Variant	rs10876986
Chromosome Location	chr12:57856667-57856668
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	RAD21	chr12:57856319-57856803	H1-hESC	embryonic stem cell:	n/a	chr12:57856613-57856632
2	YY1	chr12:57856408-57856743	GM12892	blood:	n/a	n/a
3	SMC3	chr12:57856200-57857091	SK-N-SH	brain:	n/a	chr12:57856582-57856592 chr12:57856617-57856631
4	RUNX3	chr12:57856155-57856831	GM12878	blood:	n/a	n/a
5	SP1	chr12:57852528-57856905	A549	lung:	n/a	chr12:57855088-57855100 chr12:57854788-57854797 chr12:57855421-57855430 chr12:57854019-57854032 chr12:57856662-57856671 chr12:57855543-57855552 chr12:57855232-57855244 chr12:57855089-57855099 chr12:57855429-57855443 chr12:57855571-57855580 chr12:57854556-57854565 chr12:57855541-57855553 chr12:57853860-57853872 chr12:57854024-57854036 chr12:57855089-57855098 chr12:57855570-57855582 chr12:57856000-57856009 chr12:57853899-57853911 chr12:57854788-57854797 chr12:57855233-57855247 chr12:57856151-57856163 chr12:57856152-57856161 chr12:57855594-57855608 chr12:57855090-57855099 chr12:57855547-57855561 chr12:57856000-57856014 chr12:57855999-57856011 chr12:57853861-57853871 chr12:57854546-57854560 chr12:57855232-57855244 chr12:57853861-57853870 chr12:57855570-57855582 chr12:57856152-57856166 chr12:57853659-57853668 chr12:57855567-57855581 chr12:57855572-57855581 chr12:57855542-57855551 chr12:57853154-57853161 chr12:57854024-57854036 chr12:57856153-57856162 chr12:57855090-57855099 chr12:57856001-57856010 chr12:57855085-57855099 chr12:57856525-57856539 chr12:57856151-57856163 chr12:57854788-57854798 chr12:57855999-57856011 chr12:57854025-57854034 chr12:57853836-57853850 chr12:57856152-57856162 chr12:57855232-57855243 chr12:57854021-57854035 chr12:57855114-57855127 chr12:57853901-57853910 chr12:57855089-57855099 chr12:57855088-57855100 chr12:57855950-57855964 chr12:57856000-57856010 chr12:57855543-57855552 chr12:57854557-57854566
6	CTCF	chr12:57856580-57856730	HVMF	connective:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856615-57856633
7	POLR2A	chr12:57856354-57856668	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr12:57856560-57856710	MCF-7	breast:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
9	ELK1	chr12:57856298-57856758	Hela-S3	cervix:	n/a	n/a
10	MYC	chr12:57856158-57856789	K562	blood:	n/a	n/a
11	FOXA2	chr12:57856107-57856838	A549	lung:	n/a	n/a
12	TCF12	chr12:57855871-57856773	A549	lung:	n/a	chr12:57856056-57856063
13	ESRRA	chr12:57856023-57857009	GM12878	blood:	n/a	n/a
14	RAD21	chr12:57856448-57856774	K562	blood:	n/a	chr12:57856613-57856632
15	GABPA	chr12:57856471-57856780	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr12:57856090-57856767	SK-N-SH_RA	brain:	n/a	n/a
17	IRF1	chr12:57856264-57856759	K562	blood:	n/a	chr12:57856474-57856486
18	CTCF	chr12:57856560-57856710	GM12870	blood:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
19	BCLAF1	chr12:57856231-57856797	GM12878	blood:	n/a	n/a
20	CTCF	chr12:57856361-57856795	H1-hESC	embryonic stem cell:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
21	RAD21	chr12:57856490-57856709	K562	blood:	n/a	chr12:57856613-57856632
22	CTCF	chr12:57856560-57856710	NHDF-neo	bronchial:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
23	CTCF	chr12:57856600-57856750	HFF-Myc	foreskin:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856615-57856633
24	ZNF143	chr12:57856110-57856800	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAFK	chr12:57856181-57856749	Hela-S3	cervix:	n/a	n/a
26	BCLAF1	chr12:57856245-57856829	GM12878	blood:	n/a	n/a
27	ELF1	chr12:57856510-57856749	HepG2	liver:	n/a	n/a
28	MXI1	chr12:57856261-57856791	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr12:57856560-57856710	SAEC	small airway:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
30	USF1	chr12:57856463-57856706	H1-hESC	embryonic stem cell:	n/a	n/a
31	PML	chr12:57856471-57856697	GM12878	blood:	n/a	n/a
32	POLR2A	chr12:57856466-57856697	A549	lung:	n/a	n/a
33	EP300	chr12:57856328-57856698	GM12878	blood:	n/a	n/a
34	BRCA1	chr12:57856188-57856736	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr12:57856560-57856710	BJ	skin:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
36	CTCF	chr12:57856520-57856670	GM12867	blood:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
37	CTCF	chr12:57856540-57856690	NB4	blood:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
38	CTCF	chr12:57856540-57856690	AG09319	gingival:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
39	TAF7	chr12:57856092-57856779	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr12:57856300-57856753	H1-hESC	embryonic stem cell:	n/a	n/a
41	TAF1	chr12:57856326-57856742	GM12878	blood:	n/a	n/a
42	FOXA2	chr12:57856454-57856706	HepG2	liver:	n/a	n/a
43	STAT1	chr12:57856239-57856796	GM12878	blood:	n/a	n/a
44	JUND	chr12:57854615-57856806	A549	lung:	n/a	chr12:57855936-57855945 chr12:57855597-57855606 chr12:57855938-57855945 chr12:57855935-57855946 chr12:57856002-57856011 chr12:57855935-57855947 chr12:57856274-57856288
45	TBL1XR1	chr12:57856412-57856717	K562	blood:	n/a	n/a
46	CTCF	chr12:57853855-57857058	A549	lung:	n/a	chr12:57856610-57856631 chr12:57854445-57854463 chr12:57854447-57854468 chr12:57854448-57854457 chr12:57856617-57856630 chr12:57854448-57854461 chr12:57856579-57856592 chr12:57856615-57856633
47	CTCF	chr12:57856540-57856690	GM12867	blood:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
48	CTCF	chr12:57856374-57856768	H1-hESC	embryonic stem cell:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
49	SIN3A	chr12:57856272-57856794	GM12878	blood:	n/a	chr12:57856650-57856663
50	CTCF	chr12:57856540-57856690	AG09309	skin:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633

No.	Distal block	Cell Line	Cell type
1	chr12:57856465..57858334-chr12:57867233..57870220,2	MCF-7	breast:
2	chr12:57855324..57857821-chr12:57881155..57883248,2	MCF-7	breast:
3	chr12:57849885..57859254-chr12:57908711..57915821,16	K562	blood:
4	chr12:57855142..57857395-chr12:57860962..57863336,2	K562	blood:
5	chr12:57854130..57857750-chr12:57881459..57884101,5	K562	blood:
6	chr12:57701098..57701821-chr12:57856115..57856743,3	MCF-7	breast:
7	chr12:57856220..57856940-chr12:58129447..58130061,2	MCF-7	breast:
8	chr12:57852034..57858739-chr12:57911478..57917144,8	MCF-7	breast:
9	chr12:57633619..57639143-chr12:57853203..57857806,7	K562	blood:
10	chr12:57856136..57857070-chr12:58020257..58020872,2	K562	blood:
11	chr12:57820715..57827591-chr12:57847165..57857509,18	K562	blood:
12	chr12:57850154..57858218-chr12:57910899..57919538,20	K562	blood:
13	chr12:57855242..57858206-chr12:57882251..57883801,2	K562	blood:

Variant related genes	Relation type
GLI1	TF binding region
ENSG00000175197	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000258001	Chromatin interaction
ENSG00000185633	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000166987	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10783826	0.82[ASN][1000 genomes]
rs10783827	0.90[ASN][1000 genomes]
rs10783828	0.81[ASN][1000 genomes]
rs10876987	0.83[ASN][1000 genomes]
rs11544238	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2228224	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2228225	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292657	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3782125	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3782126	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817474	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817475	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3825077	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760148	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760255	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7309467	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS 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	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv8974	chr12:57852779-57865881	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57852400-57856800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:57853000-57856800	Active TSS	Brain Substantia Nigra	brain
3	chr12:57853000-57856800	Active TSS	Fetal Kidney	kidney
4	chr12:57854000-57856800	Enhancers	Spleen	Spleen
5	chr12:57854200-57856800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr12:57854600-57856800	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr12:57855000-57856800	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr12:57855000-57856800	Flanking Active TSS	Dnd41	blood
9	chr12:57855000-57856800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
10	chr12:57855200-57856800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr12:57855200-57856800	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr12:57855400-57856800	Active TSS	Colon Smooth Muscle	Colon
13	chr12:57855400-57857000	Active TSS	Hela-S3	cervix
14	chr12:57855600-57856800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:57855600-57856800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr12:57855600-57856800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
17	chr12:57855600-57856800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr12:57855800-57856800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr12:57856200-57856800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr12:57856200-57856800	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr12:57856200-57856800	Active TSS	Fetal Brain Female	brain
22	chr12:57856200-57856800	Flanking Active TSS	Stomach Mucosa	stomach
23	chr12:57856200-57857600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:57856200-57863200	Weak transcription	Gastric	stomach
25	chr12:57856400-57856800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:57856400-57856800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:57856400-57856800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:57856400-57856800	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr12:57856400-57856800	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr12:57856400-57856800	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr12:57856400-57856800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr12:57856400-57856800	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr12:57856400-57856800	Flanking Active TSS	HepG2	liver
34	chr12:57856400-57856800	Flanking Active TSS	K562	blood
35	chr12:57856600-57856800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr12:57856600-57856800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr12:57856600-57856800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:57856600-57856800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:57856600-57856800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr12:57856600-57856800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:57856600-57856800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:57856600-57856800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:57856600-57856800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:57856600-57856800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:57856600-57856800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:57856600-57856800	Enhancers	Liver	Liver
47	chr12:57856600-57856800	Enhancers	Brain Angular Gyrus	brain
48	chr12:57856600-57856800	Enhancers	Brain Anterior Caudate	brain
49	chr12:57856600-57856800	Enhancers	Brain Cingulate Gyrus	brain
50	chr12:57856600-57856800	Enhancers	Colonic Mucosa	Colon

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