Variant report

Variant	rs7295923
Chromosome Location	chr12:45269284-45269285
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	TBP	chr12:45269018-45270675	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr12:45269089-45269672	ECC-1	luminal epithelium:	n/a	n/a
3	TAF1	chr12:45268863-45270739	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:45268975-45270442	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZBTB7A	chr12:45269031-45271159	ECC-1	luminal epithelium:	n/a	chr12:45270797-45270806 chr12:45269905-45269913
6	ZBTB7A	chr12:45268901-45271105	ECC-1	luminal epithelium:	n/a	chr12:45270797-45270806 chr12:45269905-45269913
7	MXI1	chr12:45268594-45271198	SK-N-SH	brain:	n/a	n/a
8	REST	chr12:45269036-45271162	H1-neurons	neurons:	n/a	chr12:45270531-45270544 chr12:45270779-45270788 chr12:45270351-45270365
9	GATA2	chr12:45268654-45269926	SH-SY5Y	brain:	n/a	chr12:45268852-45268860
10	POLR2A	chr12:45269185-45270789	H1-neurons	neurons:	n/a	n/a
11	MAX	chr12:45269268-45271034	ECC-1	luminal epithelium:	n/a	n/a
12	SIN3A	chr12:45268716-45271054	H1-hESC	embryonic stem cell:	n/a	chr12:45269887-45269898 chr12:45270781-45270789 chr12:45268990-45269004
13	MAX	chr12:45269216-45271039	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr12:45268740-45270705	H1-hESC	embryonic stem cell:	n/a	n/a
15	E2F6	chr12:45269235-45269994	H1-hESC	embryonic stem cell:	n/a	chr12:45269727-45269734 chr12:45269727-45269734 chr12:45269726-45269734 chr12:45269727-45269734
16	ZNF263	chr12:45268711-45269924	HEK293-T-REx	kidney:	n/a	chr12:45269265-45269274
17	RAD21	chr12:45268792-45269500	H1-hESC	embryonic stem cell:	n/a	n/a
18	CHD1	chr12:45268922-45269885	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
NELL2	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10506258	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs10785535	0.91[JPT][hapmap]
rs10785539	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10880695	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10880696	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10880704	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11182706	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11615964	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12822444	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs1376126	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1506676	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1506678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1506679	0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1506680	0.85[ASN][1000 genomes]
rs1876241	0.81[ASN][1000 genomes]
rs2408084	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2408085	0.83[CHB][hapmap]
rs2465108	0.82[ASN][1000 genomes]
rs2465110	0.83[ASN][1000 genomes]
rs2658948	0.84[ASN][1000 genomes]
rs2658954	0.81[ASN][1000 genomes]
rs2939697	0.84[ASN][1000 genomes]
rs2939698	0.85[ASN][1000 genomes]
rs374144	0.91[JPT][hapmap]
rs7304472	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305124	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7952764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7953663	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7963606	0.87[ASN][1000 genomes]
rs7979717	0.87[EUR][1000 genomes];0.94[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	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
2	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7295923	DBX2	cis	Skin Sun Exposed Lower leg	GTEx
rs7295923	RP11-478B9.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45264800-45271200	Active TSS	Fetal Brain Male	brain
2	chr12:45266000-45270600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
3	chr12:45266800-45270800	Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr12:45267200-45271000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:45267200-45271400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:45267800-45271000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
7	chr12:45268000-45270000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr12:45268000-45270800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:45268000-45270800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:45268000-45271000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:45268000-45271200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr12:45268200-45271200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr12:45268400-45269400	Bivalent/Poised TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:45268400-45269600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:45268600-45269400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:45268600-45269400	Bivalent/Poised TSS	Fetal Kidney	kidney
17	chr12:45268600-45269600	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
18	chr12:45268600-45269600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
19	chr12:45268600-45269800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr12:45268600-45270000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
21	chr12:45268600-45270400	Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr12:45268600-45270400	Active TSS	Right Atrium	heart
23	chr12:45268600-45270600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:45268600-45271000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:45268600-45271200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr12:45268800-45269400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:45268800-45269400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr12:45268800-45269400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
29	chr12:45268800-45269400	Bivalent Enhancer	Fetal Heart	heart
30	chr12:45268800-45269400	Bivalent Enhancer	Placenta	Placenta
31	chr12:45268800-45269400	Bivalent Enhancer	Small Intestine	intestine
32	chr12:45268800-45269600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr12:45268800-45269600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
34	chr12:45268800-45269600	Flanking Active TSS	Psoas Muscle	Psoas
35	chr12:45268800-45269600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
36	chr12:45268800-45269600	Bivalent/Poised TSS	NHDF-Ad	bronchial
37	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
38	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
41	chr12:45268800-45269800	Enhancers	Lung	lung
42	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
43	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
44	chr12:45268800-45269800	Bivalent Enhancer	Stomach Mucosa	stomach
45	chr12:45268800-45269800	Enhancers	Spleen	Spleen
46	chr12:45268800-45269800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
47	chr12:45268800-45270000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:45268800-45270000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:45268800-45270000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:45268800-45270000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links