Variant report

Variant	rs772257
Chromosome Location	chr12:56121194-56121195
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	POLR2A	chr12:56121103-56124569	IMR90	lung:	n/a	n/a
2	POLR2A	chr12:56113532-56124497	U87	brain:	n/a	n/a
3	CHD1	chr12:56120323-56124349	IMR90	lung:	n/a	n/a
4	POLR2A	chr12:56120371-56121341	K562	blood:	n/a	n/a
5	POLR2A	chr12:56120605-56121224	K562	blood:	n/a	n/a
6	MXI1	chr12:56121169-56124795	SK-N-SH	brain:	n/a	chr12:56122967-56122976 chr12:56122965-56122974 chr12:56122967-56122976 chr12:56122965-56122974
7	POLR2A	chr12:56120298-56122466	U87	brain:	n/a	n/a
8	NR2F2	chr12:56121192-56122038	K562	blood:	n/a	n/a
9	MXI1	chr12:56120957-56124566	IMR90	lung:	n/a	chr12:56122967-56122976 chr12:56122965-56122974 chr12:56122967-56122976 chr12:56122965-56122974
10	HCFC1	chr12:56121019-56124496	Hela-S3	cervix:	n/a	n/a
11	HEY1	chr12:56120947-56121195	K562	blood:	n/a	n/a
12	MAZ	chr12:56121069-56124631	IMR90	lung:	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
13	POLR2A	chr12:56120835-56121300	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr12:56113243-56124503	U87	brain:	n/a	n/a
15	POLR2A	chr12:56120252-56122128	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56119665..56125098-chr12:56220794..56225708,11	MCF-7	breast:
2	chr12:56120003..56122736-chr12:56659216..56661326,3	K562	blood:
3	chr12:56120093..56124486-chr12:56434488..56437037,3	K562	blood:
4	chr12:56120864..56122982-chr12:56435772..56437272,2	MCF-7	breast:
5	chr12:56120515..56122201-chr12:56332595..56334238,2	K562	blood:
6	chr12:56120851..56123825-chr12:56659216..56662167,3	K562	blood:
7	chr12:56117197..56125255-chr12:56135299..56142277,21	K562	blood:
8	chr12:56098994..56103683-chr12:56119699..56126107,8	MCF-7	breast:
9	chr12:56121086..56122985-chr12:56327062..56330070,3	MCF-7	breast:
10	chr12:56120734..56123554-chr12:56508983..56512643,4	K562	blood:
11	chr12:56104896..56106917-chr12:56120568..56123344,2	MCF-7	breast:
12	chr12:56120240..56124369-chr12:56508983..56513755,7	K562	blood:
13	chr12:56120591..56123197-chr12:56472700..56474357,3	MCF-7	breast:
14	chr12:56120533..56123958-chr12:56496918..56499602,3	K562	blood:
15	chr12:56119392..56124555-chr12:56134719..56139155,10	MCF-7	breast:
16	chr12:56118873..56123597-chr12:56135421..56141775,11	K562	blood:
17	chr12:56120972..56124195-chr12:56135682..56138639,8	MCF-7	breast:
18	chr12:56120505..56122635-chr12:56345271..56347933,2	K562	blood:
19	chr12:56120587..56125243-chr12:56320195..56323478,6	MCF-7	breast:
20	chr12:56099553..56102772-chr12:56120884..56124385,4	K562	blood:
21	chr12:56119294..56126638-chr12:56434111..56441706,13	K562	blood:

Variant related genes	Relation type
ENSG00000258056	TF binding region
CD63	TF binding region
ENSG00000065361	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000135469	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000257390	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000135424	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1466512	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1681085	1.00[AMR][1000 genomes]
rs1725358	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs1871999	1.00[AMR][1000 genomes]
rs2449476	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2462935	1.00[AFR][1000 genomes]
rs2462938	1.00[AMR][1000 genomes]
rs2694008	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2694015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2887997	1.00[AMR][1000 genomes]
rs4759012	1.00[AMR][1000 genomes]
rs4759202	1.00[AMR][1000 genomes]
rs55884432	1.00[AMR][1000 genomes]
rs6581083	1.00[AMR][1000 genomes]
rs7294345	1.00[AMR][1000 genomes]
rs7305623	1.00[MEX][hapmap]
rs7310325	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs772250	1.00[AMR][1000 genomes]
rs772251	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs772252	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs772253	1.00[AMR][1000 genomes]
rs772256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772259	1.00[AMR][1000 genomes]
rs772260	1.00[AMR][1000 genomes]
rs772261	1.00[AMR][1000 genomes]
rs7956337	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs7963379	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs812230	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv559007	chr12:56118833-56121194	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
6	nsv559008	chr12:56119594-56121194	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv559009	chr12:56119683-56121194	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	19 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	chr12:56115400-56121200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56116600-56121800	Transcr. at gene 5' and 3'	HSMM	muscle
3	chr12:56116600-56122200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:56116800-56122200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:56117000-56121200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:56117200-56121400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:56117400-56121200	Enhancers	Fetal Heart	heart
8	chr12:56117600-56122000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
9	chr12:56117800-56121200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:56117800-56122200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:56118200-56121200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:56118200-56121600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
13	chr12:56118800-56121600	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:56118800-56122000	Transcr. at gene 5' and 3'	NHLF	lung
15	chr12:56119000-56121400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
16	chr12:56119000-56121600	Transcr. at gene 5' and 3'	Osteobl	bone
17	chr12:56119400-56121200	Transcr. at gene 5' and 3'	Right Ventricle	heart
18	chr12:56119400-56121200	Weak transcription	Thymus	Thymus
19	chr12:56119600-56121600	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
20	chr12:56119800-56122000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
21	chr12:56120200-56121200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:56120200-56121200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:56120400-56121200	Enhancers	Primary B cells from cord blood	blood
24	chr12:56120400-56121200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:56120400-56121200	Genic enhancers	Brain Angular Gyrus	brain
26	chr12:56120400-56121200	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
27	chr12:56120400-56121200	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
28	chr12:56120400-56121200	Transcr. at gene 5' and 3'	HMEC	breast
29	chr12:56120400-56121200	Transcr. at gene 5' and 3'	NH-A	brain
30	chr12:56120400-56121400	Enhancers	Primary hematopoietic stem cells	blood
31	chr12:56120400-56121400	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
32	chr12:56120400-56121400	Genic enhancers	Dnd41	blood
33	chr12:56120400-56121600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:56120400-56121800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr12:56120400-56122000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:56120400-56122000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
37	chr12:56120400-56122000	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
38	chr12:56120400-56122000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
39	chr12:56120400-56122200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
40	chr12:56120600-56121200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:56120600-56121200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
42	chr12:56120600-56121200	Transcr. at gene 5' and 3'	K562	blood
43	chr12:56120600-56121400	Genic enhancers	Primary monocytes fromperipheralblood	blood
44	chr12:56120600-56121400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr12:56120600-56121400	Genic enhancers	Spleen	Spleen
46	chr12:56120600-56121400	Transcr. at gene 5' and 3'	A549	lung
47	chr12:56120600-56121400	Transcr. at gene 5' and 3'	Hela-S3	cervix
48	chr12:56120600-56121600	Genic enhancers	Primary T cells fromperipheralblood	blood
49	chr12:56120600-56121600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr12:56120600-56121600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin

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