Variant report

Variant	rs13376734
Chromosome Location	chr10:52381154-52381155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr10:52380757-52381610	HEK293	kidney:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52361423..52364078-chr10:52378639..52381362,2	K562	blood:
2	chr10:52075208..52077138-chr10:52380386..52382972,2	K562	blood:
3	chr10:52369146..52370926-chr10:52380140..52382580,2	MCF-7	breast:
4	chr10:52371171..52374113-chr10:52380759..52382982,2	MCF-7	breast:
5	chr10:52358660..52367648-chr10:52378481..52386533,25	MCF-7	breast:
6	chr10:52174976..52177960-chr10:52379518..52382234,2	K562	blood:
7	chr10:52378282..52382247-chr10:52382625..52385315,3	K562	blood:
8	chr10:52356810..52366659-chr10:52378806..52385975,25	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226200	TF binding region
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction
ENSG00000230036	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10218880	1.00[CHB][hapmap]
rs10218927	1.00[CHB][hapmap]
rs11006224	1.00[CHB][hapmap]
rs1212555	0.80[TSI][hapmap]
rs12243444	1.00[CHB][hapmap]
rs12262564	1.00[CHB][hapmap]
rs12358866	0.83[YRI][hapmap]
rs2064760	0.83[TSI][hapmap]
rs2208037	0.84[EUR][1000 genomes]
rs2860490	0.84[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2983352	0.80[TSI][hapmap]
rs2983362	0.83[TSI][hapmap]
rs2983363	0.84[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs2983365	0.84[EUR][1000 genomes]
rs3001853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001855	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs3001856	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001857	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001858	0.87[CEU][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3001859	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001860	0.84[EUR][1000 genomes]
rs3001861	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001864	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3001865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3001866	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001867	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001884	0.95[EUR][1000 genomes]
rs3011711	0.84[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs3011717	0.88[EUR][1000 genomes]
rs3011718	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3011719	0.86[AMR][1000 genomes]
rs3011728	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3011729	0.87[EUR][1000 genomes]
rs3011730	0.87[EUR][1000 genomes]
rs3011731	0.87[EUR][1000 genomes]
rs3011738	0.90[EUR][1000 genomes]
rs3011739	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs3011748	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3011752	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56153288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56266445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57025029	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67094247	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077555	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077589	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs7078586	0.93[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes]
rs7096920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100589	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72787008	0.87[EUR][1000 genomes]
rs72803755	0.96[EUR][1000 genomes]
rs7897345	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7904446	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908093	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13376734	CSTF2T	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52366000-52381600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr10:52367400-52381400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr10:52367600-52381400	Weak transcription	NHLF	lung
4	chr10:52367600-52381400	Weak transcription	Osteobl	bone
5	chr10:52371000-52381200	Weak transcription	Fetal Stomach	stomach
6	chr10:52371200-52381600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr10:52372600-52381600	Weak transcription	Aorta	Aorta
8	chr10:52374200-52381200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr10:52374400-52381200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr10:52374400-52381600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:52374400-52381600	Weak transcription	Spleen	Spleen
12	chr10:52374600-52381600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:52374800-52381600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr10:52375000-52381600	Weak transcription	Ovary	ovary
15	chr10:52375000-52381600	Weak transcription	Stomach Mucosa	stomach
16	chr10:52375400-52381600	Weak transcription	Left Ventricle	heart
17	chr10:52375400-52381600	Weak transcription	Psoas Muscle	Psoas
18	chr10:52375400-52381800	Weak transcription	Lung	lung
19	chr10:52376600-52381200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr10:52377000-52381600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr10:52377200-52381400	Enhancers	Primary T cells from cord blood	blood
22	chr10:52377600-52381400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr10:52377800-52381200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr10:52377800-52381200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr10:52377800-52381200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr10:52377800-52381400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr10:52377800-52381400	Enhancers	NHEK	skin
28	chr10:52378000-52381200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr10:52378000-52381200	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr10:52378000-52381400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr10:52378000-52381400	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr10:52378000-52381400	Enhancers	HMEC	breast
33	chr10:52378200-52381400	Weak transcription	HSMMtube	muscle
34	chr10:52378400-52381200	Enhancers	Fetal Thymus	thymus
35	chr10:52378400-52381400	Enhancers	Primary T cells fromperipheralblood	blood
36	chr10:52378400-52381400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr10:52378400-52381400	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr10:52378400-52381600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr10:52378400-52381600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr10:52378600-52381400	Enhancers	Fetal Heart	heart
41	chr10:52378600-52381600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr10:52378800-52381200	Enhancers	Liver	Liver
43	chr10:52378800-52381400	Enhancers	Colon Smooth Muscle	Colon
44	chr10:52378800-52381600	Enhancers	Brain Hippocampus Middle	brain
45	chr10:52379000-52381400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr10:52379000-52381400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr10:52379200-52381200	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr10:52379200-52381400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr10:52379200-52381400	Enhancers	Fetal Lung	lung
50	chr10:52379400-52381200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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