Variant report

Variant	rs7963379
Chromosome Location	chr12:56212585-56212586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr12:56210649-56212606	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr12:56211044-56213292	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:56211170-56213050	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:56210922-56213472	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr12:56211178-56213384	U87	brain:	n/a	n/a
6	TCF12	chr12:56210827-56212602	ECC-1	luminal epithelium:	n/a	chr12:56212419-56212427
7	POLR2A	chr12:56211022-56212888	K562	blood:	n/a	n/a
8	POLR2A	chr12:56210919-56212781	U87	brain:	n/a	n/a
9	POLR2A	chr12:56210591-56212796	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr12:56210676-56212702	K562	blood:	n/a	n/a
11	POLR2A	chr12:56210736-56213485	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr12:56210945-56212686	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr12:56211022-56212838	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr12:56211074-56213275	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:56211240-56213087	U87	brain:	n/a	n/a
16	POLR2A	chr12:56210979-56212617	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:56210984-56213078	GM12891	blood:	n/a	n/a
18	GABPA	chr12:56210968-56212591	MCF-7	breast:	n/a	n/a
19	POLR2A	chr12:56210834-56212963	HepG2	liver:	n/a	n/a
20	BCL3	chr12:56210901-56212764	A549	lung:	n/a	chr12:56211640-56211649 chr12:56211511-56211524
21	POLR2A	chr12:56210944-56212691	HCT-116	colon:	n/a	n/a
22	POLR2A	chr12:56211245-56212634	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr12:56211028-56213245	MCF-7	breast:	n/a	n/a
24	POLR2A	chr12:56211007-56213054	GM12892	blood:	n/a	n/a
25	POLR2A	chr12:56211293-56213281	K562	blood:	n/a	n/a
26	MAZ	chr12:56210649-56212878	IMR90	lung:	n/a	chr12:56211516-56211526
27	POLR2A	chr12:56211655-56213507	K562	blood:	n/a	n/a
28	POLR2A	chr12:56211091-56212605	GM12892	blood:	n/a	n/a
29	POLR2A	chr12:56210869-56217420	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr12:56210912-56213398	PANC-1	pancreas:	n/a	n/a
31	TCF7L2	chr12:56212312-56212663	PANC-1	pancreas:	n/a	chr12:56212392-56212408 chr12:56212342-56212352 chr12:56212392-56212408 chr12:56212555-56212569
32	POLR2A	chr12:56210957-56213369	GM12878	blood:	n/a	n/a
33	MAX	chr12:56210826-56212636	A549	lung:	n/a	chr12:56211516-56211526
34	POLR2A	chr12:56210682-56212698	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr12:56211048-56213406	GM12892	blood:	n/a	n/a
36	SIN3AK20	chr12:56210627-56212614	MCF-7	breast:	n/a	n/a
37	POLR2A	chr12:56210835-56212781	U87	brain:	n/a	n/a
38	POLR2A	chr12:56210973-56213039	GM12891	blood:	n/a	n/a
39	MXI1	chr12:56210517-56212657	IMR90	lung:	n/a	n/a
40	POLR2A	chr12:56211244-56212703	SK-N-MC	brain:	n/a	n/a
41	POLR2A	chr12:56210833-56213384	PFSK-1	brain:	n/a	n/a
42	BCL3	chr12:56210926-56212872	A549	lung:	n/a	chr12:56211640-56211649 chr12:56211511-56211524
43	HCFC1	chr12:56210602-56213504	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr12:56211188-56212954	GM12892	blood:	n/a	n/a
45	POLR2A	chr12:56210888-56212722	HUVEC	blood vessel:	n/a	n/a
46	MTA3	chr12:56210602-56212937	GM12878	blood:	n/a	n/a
47	POLR2A	chr12:56211096-56212720	GM12878	blood:	n/a	n/a
48	POLR2A	chr12:56210794-56212886	HUVEC	blood vessel:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56208117..56217611-chr12:56318345..56328982,45	MCF-7	breast:
2	chr12:56211633..56216017-chr12:56399885..56403410,4	MCF-7	breast:
3	chr12:56212308..56214556-chr12:56437662..56439315,2	MCF-7	breast:
4	chr12:56135540..56139368-chr12:56208041..56213329,11	MCF-7	breast:
5	chr12:56136952..56138818-chr12:56210059..56212920,2	MCF-7	breast:
6	chr12:56212373..56216209-chr12:56435568..56437517,3	MCF-7	breast:
7	chr12:56210044..56216553-chr12:56364276..56371676,13	MCF-7	breast:
8	chr12:56136481..56142183-chr12:56210043..56213312,6	K562	blood:
9	chr12:56208204..56214844-chr12:56359426..56363484,9	MCF-7	breast:
10	chr12:56135741..56138597-chr12:56211072..56214599,4	K562	blood:
11	chr12:56209991..56213836-chr12:56388557..56392258,6	MCF-7	breast:
12	chr12:56122035..56125892-chr12:56210581..56213887,4	K562	blood:
13	chr12:56210455..56212790-chr12:56435066..56437044,2	K562	blood:
14	chr12:56208546..56216914-chr12:56318326..56328671,24	MCF-7	breast:
15	chr12:56209486..56213209-chr12:56366653..56370251,5	MCF-7	breast:
16	chr12:56210626..56213378-chr12:56473835..56475955,2	MCF-7	breast:
17	chr12:56210232..56212783-chr4:146019358..146021941,2	MCF-7	breast:
18	chr12:56211327..56213257-chr12:56331810..56333930,2	K562	blood:
19	chr12:56210260..56213184-chr12:56348200..56352160,4	MCF-7	breast:
20	chr12:56211662..56213593-chr12:56320133..56321834,2	K562	blood:
21	chr12:56211687..56216264-chr12:56332406..56336008,6	MCF-7	breast:
22	chr12:56209963..56212805-chr12:56473917..56475602,2	MCF-7	breast:
23	chr12:56210928..56213016-chr12:57081918..57083884,2	K562	blood:
24	chr12:56210386..56214682-chr12:56319005..56323153,8	K562	blood:

No data

Variant related genes	Relation type
SARNP	TF binding region
ENSG00000170473	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000164163	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000164162	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000139531	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1466512	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1681085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1689516	1.00[MEX][hapmap]
rs1701705	1.00[MEX][hapmap]
rs1725358	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1871999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2449476	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2462938	1.00[AMR][1000 genomes]
rs2694008	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2694015	1.00[AMR][1000 genomes]
rs2887997	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4759012	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4759202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55884432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6581083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7294345	1.00[AFR][1000 genomes];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];1.00[YRI][hapmap]
rs772252	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs772253	1.00[AMR][1000 genomes]
rs772256	1.00[AMR][1000 genomes]
rs772257	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs772259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772260	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772261	1.00[AMR][1000 genomes]
rs7956337	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs808896	1.00[MEX][hapmap]
rs812230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56209800-56212600	Active TSS	H1 Cell Line	embryonic stem cell
2	chr12:56209800-56212600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:56209800-56212800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:56209800-56213000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr12:56210000-56212600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:56210000-56212600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:56210000-56212600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:56210000-56212600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:56210000-56212600	Active TSS	NHEK	skin
10	chr12:56210000-56212800	Active TSS	HMEC	breast
11	chr12:56210000-56212800	Active TSS	HSMM	muscle
12	chr12:56210200-56212600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:56210200-56212600	Active TSS	Aorta	Aorta
14	chr12:56210200-56212600	Active TSS	HSMMtube	muscle
15	chr12:56210200-56212800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:56210200-56212800	Active TSS	Right Ventricle	heart
17	chr12:56210400-56212600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr12:56210400-56212600	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr12:56210400-56212600	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr12:56210400-56212600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:56210400-56212800	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr12:56210400-56212800	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr12:56210400-56213000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr12:56210400-56213000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:56210600-56212600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:56210600-56212600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:56210600-56212600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:56210600-56212600	Active TSS	Brain Substantia Nigra	brain
29	chr12:56210600-56212600	Active TSS	Fetal Muscle Trunk	muscle
30	chr12:56210600-56212600	Active TSS	Pancreas	Pancrea
31	chr12:56210600-56212600	Active TSS	Psoas Muscle	Psoas
32	chr12:56210600-56212600	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr12:56210600-56212800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr12:56210600-56212800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:56210600-56212800	Active TSS	Lung	lung
36	chr12:56210800-56212600	Active TSS	Gastric	stomach
37	chr12:56211000-56212600	Active TSS	Thymus	Thymus
38	chr12:56211400-56212600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:56212000-56212600	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr12:56212000-56212800	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr12:56212200-56212600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr12:56212200-56212600	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr12:56212200-56212600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr12:56212200-56212600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr12:56212200-56212600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:56212200-56212600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:56212200-56212600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr12:56212200-56212600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:56212200-56212600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:56212200-56212600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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