Variant report

Variant	rs7297175
Chromosome Location	chr12:56473808-56473809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:342)
CpG islands
(count:61)
Chromatin interactive
region (count:37)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:342 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr12:56473612-56474162	HepG2	liver:	n/a	n/a
2	CTCF	chr12:56473720-56473870	AG04449	skin:	n/a	chr12:56473822-56473835
3	CTCF	chr12:56473800-56473950	HAc	cerebellar:	n/a	chr12:56473822-56473835
4	ZNF263	chr12:56472733-56474087	HEK293-T-REx	kidney:	n/a	chr12:56473849-56473870
5	MYC	chr12:56473802-56473946	MCF10A-Er-Src	breast:	n/a	n/a
6	CTCF	chr12:56473724-56473930	HepG2	liver:	n/a	chr12:56473822-56473835
7	POLR2A	chr12:56472757-56474164	Hela-S3	cervix:	n/a	n/a
8	NFIC	chr12:56473406-56474218	HepG2	liver:	n/a	n/a
9	HA-E2F1	chr12:56473490-56474267	MCF-7	breast:	n/a	chr12:56473828-56473837 chr12:56474254-56474263
10	CTCF	chr12:56473720-56473870	HFF	foreskin:	n/a	chr12:56473822-56473835
11	FOXA1	chr12:56473670-56473994	T-47D	breast:	n/a	n/a
12	CTCF	chr12:56473740-56473890	AG09319	gingival:	n/a	chr12:56473822-56473835
13	SP1	chr12:56473295-56473812	H1-hESC	embryonic stem cell:	n/a	chr12:56473306-56473318 chr12:56473306-56473317 chr12:56473761-56473771 chr12:56473603-56473617 chr12:56473307-56473321 chr12:56473357-56473368 chr12:56473307-56473316 chr12:56473308-56473317 chr12:56473306-56473318 chr12:56473307-56473317
14	HMGN3	chr12:56473644-56474351	K562	blood:	n/a	chr12:56473838-56473847
15	BHLHE40	chr12:56473638-56474111	HepG2	liver:	n/a	n/a
16	E2F6	chr12:56473600-56474279	K562	blood:	n/a	chr12:56473864-56473875 chr12:56473828-56473837 chr12:56474254-56474263
17	JUN	chr12:56473756-56474035	K562	blood:	n/a	chr12:56473840-56473849
18	EP300	chr12:56472579-56474424	ECC-1	luminal epithelium:	n/a	chr12:56472949-56472965 chr12:56472948-56472964 chr12:56473343-56473352 chr12:56472872-56472881
19	CTCF	chr12:56473760-56473910	HCPEpiC	choroid plexus:	n/a	chr12:56473822-56473835
20	MXI1	chr12:56473586-56473858	K562	blood:	n/a	n/a
21	CTCF	chr12:56473780-56473930	GM12873	blood:	n/a	chr12:56473822-56473835
22	MAX	chr12:56472501-56474945	ECC-1	luminal epithelium:	n/a	chr12:56473390-56473397
23	TBL1XR1	chr12:56473689-56473985	K562	blood:	n/a	n/a
24	MYC	chr12:56473656-56474071	MCF-7	breast:	n/a	n/a
25	CTCF	chr12:56473780-56473930	GM12875	blood:	n/a	chr12:56473822-56473835
26	MBD4	chr12:56473390-56474266	HepG2	liver:	n/a	n/a
27	TCF12	chr12:56472530-56474915	ECC-1	luminal epithelium:	n/a	chr12:56474487-56474496 chr12:56473236-56473243 chr12:56474467-56474477
28	MYC	chr12:56473389-56473879	NB4	blood:	n/a	chr12:56473390-56473397
29	E2F6	chr12:56473568-56474088	A549	lung:	n/a	chr12:56473864-56473875 chr12:56473828-56473837
30	POLR2A	chr12:56473330-56474219	K562	blood:	n/a	n/a
31	POLR2A	chr12:56473778-56475011	HepG2	liver:	n/a	n/a
32	CCNT2	chr12:56473642-56474159	K562	blood:	n/a	chr12:56473903-56473912
33	REST	chr12:56473573-56474157	HepG2	liver:	n/a	n/a
34	ATF3	chr12:56473600-56474075	K562	blood:	n/a	chr12:56473830-56473839
35	CTCF	chr12:56473660-56473810	HPF	lung:	n/a	n/a
36	CTCF	chr12:56473760-56473910	AG09309	skin:	n/a	chr12:56473822-56473835
37	MAX	chr12:56472600-56474177	A549	lung:	n/a	chr12:56473390-56473397
38	MAX	chr12:56472773-56473976	A549	lung:	n/a	chr12:56473390-56473397
39	CTCF	chr12:56473790-56473940	Kidney_OC	kidney:	n/a	chr12:56473822-56473835
40	TEAD4	chr12:56473621-56474014	K562	blood:	n/a	n/a
41	JUND	chr12:56473684-56473949	H1-hESC	embryonic stem cell:	n/a	chr12:56473840-56473849 chr12:56473838-56473849
42	ZBTB7A	chr12:56473469-56474054	K562	blood:	n/a	chr12:56474035-56474043 chr12:56473827-56473836
43	CEBPD	chr12:56473585-56474139	HepG2	liver:	n/a	n/a
44	CTCF	chr12:56473720-56473870	K562	blood:	n/a	chr12:56473822-56473835
45	YY1	chr12:56473613-56474082	K562	blood:	n/a	chr12:56473825-56473839
46	IRF1	chr12:56473325-56473943	K562	blood:	n/a	n/a
47	MYC	chr12:56472758-56474012	K562	blood:	n/a	chr12:56473390-56473397
48	GATA3	chr12:56473342-56474077	T-47D	breast:	n/a	n/a
49	CTCF	chr12:56473800-56473950	SK-N-SH_RA	brain:	n/a	chr12:56473822-56473835
50	PML	chr12:56473781-56474196	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:56473759-56473809	BJ	skin:	n/a
2	chr12:56473759-56473809	Hepatocyte	liver:	n/a
3	chr12:56473759-56473809	NHBE	bronchial:	n/a
4	chr12:56473759-56473809	SK-N-SH_RA	brain:	n/a
5	chr12:56473759-56473809	HUVEC	blood vessel:	n/a
6	chr12:56473759-56473809	SK-N-SH	brain:	n/a
7	chr12:56473759-56473809	BE2_C	brain:	n/a
8	chr12:56473759-56473809	Hela-S3	cervix:	n/a
9	chr12:56473759-56473809	ECC-1	luminal epithelium:	n/a
10	chr12:56473759-56473809	HEEpiC	esophagus:	n/a
11	chr12:56473759-56473809	AG09309	skin:	n/a
12	chr12:56473759-56473809	ovcar-3	ovarian:	n/a
13	chr12:56473759-56473809	AG04449	skin:	fetal
14	chr12:56473759-56473809	NB4	blood:	n/a
15	chr12:56473759-56473809	PANC-1	pancreas:	n/a
16	chr12:56473759-56473809	AG10803	skin:	n/a
17	chr12:56473759-56473809	GM12892	blood:	n/a
18	chr12:56473759-56473809	HRPEpiC	eye:	n/a
19	chr12:56473759-56473809	HAEpiC	amniotic membrane:	n/a
20	chr12:56473759-56473809	U87	brain:	n/a
21	chr12:56473759-56473809	IMR90	lung:	fetal
22	chr12:56473759-56473809	HCM	heart:	n/a
23	chr12:56473759-56473809	NH-A	brain:	n/a
24	chr12:56473759-56473809	AG09319	gingival:	n/a
25	chr12:56473759-56473809	T-47D	breast:	n/a
26	chr12:56473759-56473809	HIPEpiC	eye:	n/a
27	chr12:56473759-56473809	HepG2	liver:	n/a
28	chr12:56473759-56473809	CMK	blood:	n/a
29	chr12:56473759-56473809	NT2-D1	testis:	n/a
30	chr12:56473759-56473809	GM19239	blood:	n/a
31	chr12:56473759-56473809	HNPCEpiC	eye:	n/a
32	chr12:56473759-56473809	LNCaP	prostate:	n/a
33	chr12:56473759-56473809	HMEC	breast:	n/a
34	chr12:56473759-56473809	ProgFib	skin:	n/a
35	chr12:56473759-56473809	HRCEpiC	kidney:	n/a
36	chr12:56473759-56473809	HCT-116	colon:	n/a
37	chr12:56473759-56473809	MCF-7	breast:	n/a
38	chr12:56473759-56473809	MCF10A-Er-Src	breast:	n/a
39	chr12:56473759-56473809	SAEC	small airway:	n/a
40	chr12:56473759-56473809	HL-60	blood:	n/a
41	chr12:56473759-56473809	GM12891	blood:	n/a
42	chr12:56473759-56473809	PFSK-1	brain:	n/a
43	chr12:56473759-56473809	GM12878	blood:	n/a
44	chr12:56473759-56473809	Jurkat	blood:	n/a
45	chr12:56473759-56473809	HRE	kidney:	n/a
46	chr12:56473759-56473809	HEK293	kidney:	embryo
47	chr12:56473759-56473809	AoSMC	blood vessel:	n/a
48	chr12:56473759-56473809	Caco-2	colon:	n/a
49	chr12:56473759-56473809	A549	lung:	n/a
50	chr12:56473759-56473809	HCPEpiC	choroid plexus:	n/a

(count:37 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56318215..56321869-chr12:56472079..56475131,3	MCF-7	breast:
2	chr12:56120591..56123197-chr12:56472700..56474357,3	MCF-7	breast:
3	chr12:56320958..56322490-chr12:56473085..56475455,2	MCF-7	breast:
4	chr12:56471198..56482935-chr12:56506922..56516262,73	MCF-7	breast:
5	chr12:56471261..56483436-chr12:56494778..56506435,58	MCF-7	breast:
6	chr12:56390252..56392502-chr12:56472754..56475150,2	MCF-7	breast:
7	chr12:56221995..56224652-chr12:56472013..56474310,2	MCF-7	breast:
8	chr12:56319967..56322287-chr12:56473106..56474816,2	K562	blood:
9	chr12:56471332..56475358-chr12:56550630..56554454,5	MCF-7	breast:
10	chr12:56471831..56474623-chr12:56543968..56546467,2	K562	blood:
11	chr12:56435072..56437678-chr12:56471264..56476125,12	MCF-7	breast:
12	chr12:56387786..56391013-chr12:56472110..56474187,3	MCF-7	breast:
13	chr12:56473421..56475215-chr12:56613648..56616195,2	MCF-7	breast:
14	chr12:56473103..56475967-chr12:56549779..56553082,5	MCF-7	breast:
15	chr12:56434525..56442579-chr12:56471686..56475431,10	K562	blood:
16	chr12:56390059..56391056-chr12:56473265..56474184,2	K562	blood:
17	chr12:56471798..56475584-chr12:56544179..56549010,6	MCF-7	breast:
18	chr12:56473548..56475475-chr12:56582788..56585025,2	K562	blood:
19	chr12:56472058..56475455-chr12:56477194..56480758,7	K562	blood:
20	chr12:56473182..56475897-chr12:56486719..56489015,2	K562	blood:
21	chr11:1591819..1593774-chr12:56472377..56474644,2	MCF-7	breast:
22	chr12:56473732..56475652-chr12:57482023..57483860,2	MCF-7	breast:
23	chr12:56470948..56480058-chr12:56507665..56513741,17	K562	blood:
24	chr12:56471914..56476515-chr12:56581933..56586574,4	MCF-7	breast:
25	chr12:56473664..56475878-chr12:56486736..56489717,2	MCF-7	breast:
26	chr12:56363280..56366159-chr12:56473026..56475603,2	MCF-7	breast:
27	chr12:56434525..56442579-chr12:56469196..56475242,12	K562	blood:
28	chr12:56471291..56475668-chr12:56497220..56500908,8	K562	blood:
29	chr12:56472813..56474332-chr12:56684204..56686935,2	MCF-7	breast:
30	chr12:56473597..56475914-chr12:56490066..56491584,2	MCF-7	breast:
31	chr12:56434164..56442518-chr12:56471459..56476251,24	MCF-7	breast:
32	chr12:56473370..56473919-chr12:56497597..56498318,2	MCF-7	breast:
33	chr12:56472606..56473813-chr12:56497510..56498516,3	MCF-7	breast:
34	chr12:56472620..56475817-chr12:56544405..56546973,4	MCF-7	breast:
35	chr12:56472197..56476808-chr12:56477200..56483474,8	K562	blood:
36	chr12:56367265..56369715-chr12:56472830..56474688,3	MCF-7	breast:
37	chr12:56472852..56474352-chr15:72409607..72411955,2	MCF-7	breast:

No data

Variant related genes	Relation type
ERBB3	TF binding region
ERBB3	CpG island
ENSG00000182796	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000257553	Chromatin interaction
ENSG00000092841	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000066933	Chromatin interaction
ENSG00000258345	Chromatin interaction
ENSG00000139531	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000257809	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000233930	Chromatin interaction
ENSG00000166192	Chromatin interaction
ENSG00000196465	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000257411	Chromatin interaction
ENSG00000184545	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10876864	0.80[EUR][1000 genomes]
rs10876870	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11171739	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1131017	0.83[EUR][1000 genomes]
rs2271194	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2292239	0.86[ASN][1000 genomes]
rs2640562	0.86[ASN][1000 genomes]
rs3741499	0.91[ASN][1000 genomes]
rs4759229	0.88[ASN][1000 genomes]
rs705696	0.87[ASN][1000 genomes]
rs7312770	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7971751	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs877636	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS 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 target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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 target site	189 gene(s)	inside rSNPs	diseases
3	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7297175	DEFB124	trans	lymphoblastoid	RTeQTL
rs7297175	RPS26	cis	multi-tissue	Pritchard
rs7297175	RAB5B	cis	Muscle Skeletal	GTEx
rs7297175	RPS26	cis	Nerve Tibial	GTEx
rs7297175	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs7297175	SUOX	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56472400-56474800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr12:56472400-56475000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:56472600-56474000	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr12:56472600-56474000	Active TSS	Muscle Satellite Cultured Cells	--
5	chr12:56472600-56474000	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr12:56472600-56474600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr12:56472600-56474600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:56472600-56474600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:56472600-56474600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:56472600-56474800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:56472600-56474800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:56472600-56475000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr12:56472600-56475200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:56472600-56475600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:56472600-56476000	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr12:56472600-56477400	Active TSS	Brain Cingulate Gyrus	brain
17	chr12:56472800-56474000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:56472800-56474000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:56472800-56474000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
20	chr12:56472800-56474000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:56472800-56474000	Active TSS	Colonic Mucosa	Colon
22	chr12:56472800-56474000	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr12:56472800-56474000	Active TSS	Esophagus	oesophagus
24	chr12:56472800-56474000	Active TSS	Fetal Intestine Large	intestine
25	chr12:56472800-56474000	Flanking Active TSS	Placenta	Placenta
26	chr12:56472800-56474000	Active TSS	Left Ventricle	heart
27	chr12:56472800-56474000	Active TSS	Lung	lung
28	chr12:56472800-56474000	Active TSS	Ovary	ovary
29	chr12:56472800-56474000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr12:56472800-56474000	Active TSS	Hela-S3	cervix
31	chr12:56472800-56474000	Active TSS	NHDF-Ad	bronchial
32	chr12:56472800-56474000	Active TSS	NHLF	lung
33	chr12:56472800-56474200	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr12:56472800-56474200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:56472800-56474200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
36	chr12:56472800-56474200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
37	chr12:56472800-56474200	Active TSS	Primary T cells from cord blood	blood
38	chr12:56472800-56474200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr12:56472800-56474200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:56472800-56474200	Active TSS	A549	lung
41	chr12:56472800-56474400	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr12:56472800-56474400	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
43	chr12:56472800-56474400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:56472800-56474400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr12:56472800-56474400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:56472800-56474600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:56472800-56474600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
48	chr12:56472800-56474600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
49	chr12:56472800-56474600	Flanking Active TSS	HMEC	breast
50	chr12:56472800-56474600	Active TSS	NHEK	skin

The 2.0 version of rSNPBase

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