Variant report

Variant	rs4965225
Chromosome Location	chr15:99793635-99793636
allele	A/G
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	TCF12	chr15:99793581-99794455	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr15:99793538-99794396	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr15:99793514-99794557	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr15:99793567-99794521	SK-N-SH	brain:	n/a	n/a
5	EP300	chr15:99793610-99794309	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr15:99793575-99794354	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99788127..99791108-chr15:99792243..99793962,2	K562	blood:
2	chr15:99788127..99790475-chr15:99792462..99794073,2	K562	blood:

Variant related genes	Relation type
TTC23	TF binding region
ENSG00000264771	TF binding region
HSP90B2P	TF binding region
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1033036	0.86[YRI][hapmap]
rs10794475	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10902543	0.81[YRI][hapmap]
rs10902544	0.87[YRI][hapmap]
rs11853278	0.89[YRI][hapmap]
rs12592075	0.86[YRI][hapmap]
rs12906357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12913897	0.82[YRI][hapmap]
rs1876927	0.86[YRI][hapmap]
rs2089709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2136627	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6598229	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6598230	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6598237	0.86[YRI][hapmap]
rs7162949	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7168227	0.82[YRI][hapmap]
rs7169906	0.82[YRI][hapmap]
rs7171205	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171210	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171217	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7182425	0.89[YRI][hapmap]
rs7182675	0.86[YRI][hapmap]
rs8040850	0.86[YRI][hapmap]
rs8041923	0.82[YRI][hapmap]
rs8042249	0.86[YRI][hapmap]
rs8042667	0.86[YRI][hapmap]
rs9920227	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9920437	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
13	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
15	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4965225	TTC23	cis	parietal	SCAN
rs4965225	TTC23	cis	lymphoblastoid	seeQTL
rs4965225	SYNM	cis	parietal	SCAN
rs4965225	NR2F2	cis	parietal	SCAN
rs4965225	TTC23	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99792200-99802800	Weak transcription	Esophagus	oesophagus
2	chr15:99792200-99807400	Weak transcription	Ovary	ovary
3	chr15:99792200-99846400	Weak transcription	Lung	lung
4	chr15:99792400-99793800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:99792400-99804200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:99792600-99793800	Enhancers	Osteobl	bone
7	chr15:99792600-99794000	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr15:99792600-99794000	Enhancers	Spleen	Spleen
9	chr15:99792600-99794200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr15:99792600-99794200	Enhancers	Small Intestine	intestine
11	chr15:99792600-99795000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:99792600-99832200	Weak transcription	Aorta	Aorta
13	chr15:99792800-99793800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:99792800-99793800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:99792800-99793800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:99792800-99793800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:99792800-99793800	Weak transcription	Psoas Muscle	Psoas
18	chr15:99792800-99793800	Weak transcription	Stomach Mucosa	stomach
19	chr15:99792800-99793800	Weak transcription	HSMMtube	muscle
20	chr15:99792800-99793800	Enhancers	NHDF-Ad	bronchial
21	chr15:99792800-99794000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr15:99792800-99794000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:99792800-99794000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr15:99792800-99794000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr15:99792800-99794000	Enhancers	Brain Anterior Caudate	brain
26	chr15:99792800-99794200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr15:99792800-99794200	Enhancers	Fetal Thymus	thymus
28	chr15:99792800-99794200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr15:99792800-99794200	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr15:99792800-99794400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:99792800-99794400	Enhancers	Primary B cells from cord blood	blood
32	chr15:99792800-99794400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:99792800-99794600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:99792800-99794800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr15:99792800-99796400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:99792800-99796400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:99792800-99798400	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:99792800-99801600	Weak transcription	Fetal Stomach	stomach
39	chr15:99792800-99802800	Weak transcription	A549	lung
40	chr15:99792800-99804200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:99792800-99804600	Weak transcription	Placenta	Placenta
42	chr15:99792800-99847000	Weak transcription	Right Ventricle	heart
43	chr15:99793000-99793800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr15:99793000-99794000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:99793000-99794000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:99793000-99794000	Weak transcription	Colonic Mucosa	Colon
47	chr15:99793000-99794000	Enhancers	Thymus	Thymus
48	chr15:99793000-99794200	Enhancers	Primary T cells from cord blood	blood
49	chr15:99793000-99794200	Enhancers	Primary hematopoietic stem cells	blood
50	chr15:99793000-99794200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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