Variant report

Variant	rs3782126
Chromosome Location	chr12:57856933-57856934
allele	A/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	SMC3	chr12:57856200-57857091	SK-N-SH	brain:	n/a	chr12:57856582-57856592 chr12:57856617-57856631
2	ESRRA	chr12:57856023-57857009	GM12878	blood:	n/a	n/a
3	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
4	CTCF	chr12:57856059-57857039	HCT-116	colon:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
5	CTCF	chr12:57856866-57856983	GM12892	blood:	n/a	n/a
6	RAD21	chr12:57856298-57856956	MCF-7	breast:	n/a	chr12:57856613-57856632
7	RAD21	chr12:57856022-57857031	HCT-116	colon:	n/a	chr12:57856613-57856632
8	RAD21	chr12:57856209-57856963	A549	lung:	n/a	chr12:57856613-57856632
9	TCF12	chr12:57852429-57856996	A549	lung:	n/a	chr12:57854335-57854342 chr12:57856056-57856063
10	EBF1	chr12:57856255-57856960	GM12878	blood:	n/a	chr12:57856657-57856667 chr12:57856656-57856667 chr12:57856655-57856668 chr12:57856657-57856666 chr12:57856657-57856666
11	CTCF	chr12:57856860-57857010	GM12874	blood:	n/a	n/a
12	MAX	chr12:57854917-57856940	A549	lung:	n/a	chr12:57855792-57855801
13	HCFC1	chr12:57854691-57857048	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr12:57855970-57857049	SK-N-SH	brain:	n/a	chr12:57856610-57856631 chr12:57856617-57856630 chr12:57856579-57856592 chr12:57856615-57856633
15	MYC	chr12:57855956-57857035	A549	lung:	n/a	n/a
16	EBF1	chr12:57856238-57856942	GM12878	blood:	n/a	chr12:57856657-57856667 chr12:57856656-57856667 chr12:57856655-57856668 chr12:57856657-57856666 chr12:57856657-57856666
17	MAX	chr12:57854863-57856976	A549	lung:	n/a	chr12:57855792-57855801
18	CTCF	chr12:57856929-57856944	GM19240	blood:	n/a	n/a
19	ZBTB7A	chr12:57852281-57856952	ECC-1	luminal epithelium:	n/a	n/a
20	MAZ	chr12:57854679-57856960	IMR90	lung:	n/a	chr12:57855792-57855801
21	CTCF	chr12:57856908-57856985	GM19238	blood:	n/a	n/a
22	CTCF	chr12:57856860-57857010	HRPEpiC	eye:	n/a	n/a
23	TCF12	chr12:57855784-57857004	ECC-1	luminal epithelium:	n/a	chr12:57856056-57856063

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	chr12:57856220..57856940-chr12:58129447..58130061,2	MCF-7	breast:
7	chr12:57852034..57858739-chr12:57911478..57917144,8	MCF-7	breast:
8	chr12:57633619..57639143-chr12:57853203..57857806,7	K562	blood:
9	chr12:57856136..57857070-chr12:58020257..58020872,2	K562	blood:
10	chr12:57856862..57858591-chr12:57918787..57921199,2	MCF-7	breast:
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
ENSG00000208028	Chromatin interaction
ENSG00000185633	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000258001	Chromatin interaction
ENSG00000123329	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10783826	0.84[EUR][1000 genomes]
rs10783827	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs10783828	0.87[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10876986	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876987	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11544238	0.80[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2228224	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2228225	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228226	0.87[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs2277316	0.87[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs2277317	0.87[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs2292657	0.84[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3782125	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817474	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817475	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825077	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760255	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760259	0.87[CEU][hapmap];0.83[GIH][hapmap]
rs7309467	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[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:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57855400-57857000	Active TSS	Hela-S3	cervix
2	chr12:57856200-57857600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:57856200-57863200	Weak transcription	Gastric	stomach
4	chr12:57856600-57857000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr12:57856600-57857000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:57856600-57857000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr12:57856600-57857000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr12:57856600-57857000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr12:57856600-57857000	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr12:57856600-57857000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr12:57856600-57857000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:57856600-57857000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr12:57856600-57857000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:57856600-57857000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr12:57856600-57857000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:57856600-57857000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr12:57856600-57857000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr12:57856600-57857000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:57856600-57857000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:57856600-57857000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:57856600-57857000	Enhancers	Fetal Intestine Large	intestine
22	chr12:57856600-57857000	Enhancers	Fetal Intestine Small	intestine
23	chr12:57856600-57857000	Enhancers	Placenta	Placenta
24	chr12:57856600-57857000	Enhancers	Fetal Thymus	thymus
25	chr12:57856600-57857000	Enhancers	Ovary	ovary
26	chr12:57856600-57857000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr12:57856600-57857200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr12:57856600-57857200	Enhancers	Primary B cells from cord blood	blood
29	chr12:57856600-57857200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:57856600-57857200	Genic enhancers	Fetal Stomach	stomach
31	chr12:57856600-57857400	Enhancers	Fetal Muscle Trunk	muscle
32	chr12:57856600-57857600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:57856600-57858000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:57856600-57858000	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:57856600-57858000	Enhancers	Fetal Muscle Leg	muscle
36	chr12:57856600-57858200	Enhancers	HSMMtube	muscle
37	chr12:57856600-57858600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:57856600-57858800	Enhancers	GM12878-XiMat	blood
39	chr12:57856600-57859200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:57856600-57860600	Weak transcription	Primary T cells from cord blood	blood
41	chr12:57856600-57863200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:57856600-57865800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:57856800-57857000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
44	chr12:57856800-57857000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr12:57856800-57857000	Enhancers	H9 Cell Line	embryonic stem cell
46	chr12:57856800-57857000	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr12:57856800-57857000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
48	chr12:57856800-57857000	Enhancers	Primary hematopoietic stem cells	blood
49	chr12:57856800-57857000	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr12:57856800-57857000	Enhancers	Primary T helper cells PMA-I stimulated	--

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