Variant report

Variant	rs12097812
Chromosome Location	chr1:94309777-94309778
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	REST	chr1:94309765-94310060	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr1:94309765-94310226	HepG2	liver:	n/a	n/a
3	CEBPB	chr1:94309772-94310176	Hela-S3	cervix:	n/a	n/a
4	MYBL2	chr1:94309743-94310276	HepG2	liver:	n/a	n/a
5	TEAD4	chr1:94309763-94310285	K562	blood:	n/a	n/a
6	FOXA1	chr1:94309757-94310241	HepG2	liver:	n/a	n/a
7	CTCF	chr1:94309758-94310130	K562	blood:	n/a	chr1:94309988-94310006
8	RAD21	chr1:94309693-94310327	A549	lung:	n/a	n/a
9	SMC3	chr1:94309179-94310348	SK-N-SH	brain:	n/a	n/a
10	CEBPB	chr1:94309771-94310179	MCF-7	breast:	n/a	n/a
11	CTCF	chr1:94309777-94310095	K562	blood:	n/a	chr1:94309988-94310006
12	RAD21	chr1:94309752-94310205	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr1:94309229-94310265	SK-N-SH	brain:	n/a	chr1:94309988-94310006
14	REST	chr1:94309762-94310170	A549	lung:	n/a	n/a
15	CEBPB	chr1:94309754-94310153	K562	blood:	n/a	n/a
16	TRIM28	chr1:94309759-94310314	K562	blood:	n/a	n/a
17	CEBPB	chr1:94309772-94310206	K562	blood:	n/a	n/a
18	RAD21	chr1:94309776-94310160	MCF-7	breast:	n/a	n/a
19	RAD21	chr1:94309774-94310173	SK-N-SH_RA	brain:	n/a	n/a
20	MAX	chr1:94309769-94310132	K562	blood:	n/a	n/a
21	TEAD4	chr1:94309771-94310264	K562	blood:	n/a	n/a
22	CTCF	chr1:94309776-94310204	GM12878	blood:	n/a	chr1:94309988-94310006
23	CBX3	chr1:94309750-94310228	K562	blood:	n/a	n/a
24	POLR2A	chr1:94309659-94309794	HepG2	liver:	n/a	n/a
25	CTCF	chr1:94309757-94310135	A549	lung:	n/a	chr1:94309988-94310006
26	MXI1	chr1:94309768-94310461	SK-N-SH	brain:	n/a	n/a
27	RAD21	chr1:94309764-94310188	SK-N-SH_RA	brain:	n/a	n/a
28	ATF2	chr1:94309755-94310109	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr1:94309158-94310289	SK-N-SH	brain:	n/a	n/a
30	CTCF	chr1:94309776-94310265	HCT-116	colon:	n/a	chr1:94309988-94310006
31	CTCF	chr1:94309707-94310239	HCT-116	colon:	n/a	chr1:94309988-94310006
32	GATA1	chr1:94309687-94310363	K562	blood:	n/a	chr1:94309947-94309960 chr1:94310100-94310107
33	RAD21	chr1:94309752-94310205	H1-hESC	embryonic stem cell:	n/a	n/a
34	RFX5	chr1:94309441-94310226	IMR90	lung:	n/a	n/a
35	CEBPB	chr1:94309772-94310165	IMR90	lung:	n/a	n/a
36	RAD21	chr1:94309768-94310232	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:94094795..94095616-chr1:94309558..94310553,5	K562	blood:
2	chr1:94096672..94097335-chr1:94309478..94310673,3	K562	blood:
3	chr1:94094804..94095480-chr1:94309483..94310060,2	MCF-7	breast:
4	chr1:94307315..94310834-chr1:94315340..94316960,3	MCF-7	breast:
5	chr1:94279712..94280219-chr1:94309586..94310428,2	MCF-7	breast:

Variant related genes	Relation type
MIR760	TF binding region
ENSG00000260464	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1051394	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10874797	0.81[EUR][1000 genomes]
rs11165021	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11165022	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11165023	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11165025	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11165026	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12023010	0.92[AFR][1000 genomes]
rs12029548	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12758972	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2092698	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2092699	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2092700	0.80[EUR][1000 genomes]
rs2103784	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2143992	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2273165	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2391315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391321	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4847191	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4847263	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4847264	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6660210	0.81[EUR][1000 genomes]
rs6666633	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6681169	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6681265	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6684054	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6697189	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6703684	0.81[EUR][1000 genomes]
rs7364663	0.84[EUR][1000 genomes]
rs7513489	0.86[EUR][1000 genomes]
rs7513786	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7514828	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7517632	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7518940	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7552293	0.81[EUR][1000 genomes]
rs7555136	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7556047	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7556107	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1822452	chr1:94278128-94320233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases
2	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12097812	DNTTIP2	Cis_1M	lymphoblastoid	RTeQTL
rs12097812	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12097812	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs12097812	RP11-488P3.1	cis	lung	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94283400-94310000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:94284200-94311200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:94290200-94311400	Weak transcription	Aorta	Aorta
4	chr1:94295400-94310000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:94299400-94310200	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:94300800-94311600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:94302200-94311200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:94302200-94311200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:94303200-94310200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:94303800-94311600	Weak transcription	Gastric	stomach
11	chr1:94304000-94311200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:94304200-94311000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:94304400-94310200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:94305000-94311000	Weak transcription	Left Ventricle	heart
15	chr1:94305400-94309800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:94305600-94310000	Weak transcription	NHEK	skin
17	chr1:94305600-94310600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:94305600-94311000	Weak transcription	HSMMtube	muscle
19	chr1:94305800-94309800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:94305800-94309800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr1:94305800-94310400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:94305800-94311200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:94306200-94309800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:94306400-94309800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:94306800-94310400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:94307000-94310000	Weak transcription	Fetal Intestine Small	intestine
27	chr1:94307000-94310800	Enhancers	NH-A	brain
28	chr1:94307000-94311200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:94307000-94311200	Weak transcription	Psoas Muscle	Psoas
30	chr1:94307200-94309800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:94307200-94311200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:94307200-94311200	Enhancers	Osteobl	bone
33	chr1:94307600-94310000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:94307600-94311000	Weak transcription	Pancreas	Pancrea
35	chr1:94307600-94311800	Weak transcription	Spleen	Spleen
36	chr1:94307800-94311000	Enhancers	NHDF-Ad	bronchial
37	chr1:94308000-94311000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr1:94308000-94311000	Enhancers	HMEC	breast
39	chr1:94308000-94311000	Enhancers	NHLF	lung
40	chr1:94308000-94311200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:94308000-94311200	Enhancers	HSMM	muscle
42	chr1:94308200-94311000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:94308200-94311200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:94308400-94310400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:94308400-94311200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:94308400-94311600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:94308600-94310000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:94308800-94311200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:94308800-94311200	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr1:94309000-94311200	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links