Variant report

Variant	rs3001853
Chromosome Location	chr10:52413720-52413721
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	JUND	chr10:52413533-52413853	K562	blood:	n/a	n/a
2	UBTF	chr10:52413022-52413877	K562	blood:	n/a	n/a
3	MAFF	chr10:52413603-52413785	K562	blood:	n/a	chr10:52413704-52413718
4	MYC	chr10:52413714-52414001	K562	blood:	n/a	n/a
5	MAFK	chr10:52413694-52413770	HepG2	liver:	n/a	chr10:52413704-52413718 chr10:52413701-52413721 chr10:52413705-52413714 chr10:52413703-52413719 chr10:52413705-52413715 chr10:52413700-52413715
6	MAFK	chr10:52413623-52413852	K562	blood:	n/a	chr10:52413704-52413718 chr10:52413701-52413721 chr10:52413705-52413714 chr10:52413703-52413719 chr10:52413705-52413715 chr10:52413700-52413715

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52382192..52390666-chr10:52409582..52414601,12	MCF-7	breast:
2	chr10:52389046..52395992-chr10:52408718..52416095,10	K562	blood:

Variant related genes	Relation type
ENSG00000231345	TF binding region
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction
ENSG00000231588	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10218880	1.00[CHB][hapmap]
rs10218927	1.00[CHB][hapmap]
rs11006224	1.00[CHB][hapmap]
rs12243444	1.00[CHB][hapmap]
rs12262564	1.00[CHB][hapmap]
rs12358866	0.83[YRI][hapmap]
rs13376734	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]
rs2064760	0.86[TSI][hapmap]
rs2208037	0.82[EUR][1000 genomes]
rs2860490	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2983352	0.83[TSI][hapmap]
rs2983362	0.86[TSI][hapmap]
rs2983363	0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2983365	0.82[EUR][1000 genomes]
rs3001855	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs3001856	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001857	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001858	0.87[CEU][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3001859	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001860	0.86[EUR][1000 genomes]
rs3001861	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001864	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3001865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3001866	0.87[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001867	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001884	0.98[EUR][1000 genomes]
rs3011711	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs3011717	0.90[EUR][1000 genomes]
rs3011718	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3011719	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3011728	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3011729	0.89[EUR][1000 genomes]
rs3011730	0.89[EUR][1000 genomes]
rs3011731	0.89[EUR][1000 genomes]
rs3011738	0.92[EUR][1000 genomes]
rs3011739	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3011748	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3011752	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56153288	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56266445	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57025029	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67094247	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074349	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077555	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077589	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7078586	0.93[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs7096920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100589	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72787008	0.90[EUR][1000 genomes]
rs72803755	0.97[EUR][1000 genomes]
rs7897345	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[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]
rs7904446	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908093	0.93[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	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
2	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
3	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
4	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
5	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
6	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
7	nsv895393	chr10:52413720-52530819	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3001853	CSTF2T	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52410000-52413800	Enhancers	Fetal Intestine Large	intestine
2	chr10:52410400-52414800	Enhancers	K562	blood
3	chr10:52411200-52419200	Weak transcription	Fetal Intestine Small	intestine
4	chr10:52411800-52414000	Enhancers	HUVEC	blood vessel
5	chr10:52412200-52414200	Enhancers	Primary B cells from peripheral blood	blood
6	chr10:52412200-52414800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr10:52412800-52413800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:52412800-52413800	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr10:52412800-52413800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr10:52412800-52413800	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr10:52412800-52414000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr10:52412800-52414000	Enhancers	Primary T cells from cord blood	blood
13	chr10:52412800-52414000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr10:52412800-52414000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr10:52412800-52414000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr10:52412800-52414000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr10:52412800-52414200	Enhancers	Adipose Nuclei	Adipose
18	chr10:52412800-52414800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr10:52413000-52413800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr10:52413000-52413800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:52413000-52413800	Enhancers	Fetal Thymus	thymus
22	chr10:52413000-52414000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr10:52413200-52414400	Weak transcription	Liver	Liver
24	chr10:52413200-52414400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr10:52413400-52413800	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr10:52413400-52414000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr10:52413400-52414000	Enhancers	Primary B cells from cord blood	blood
28	chr10:52413400-52414600	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr10:52413400-52414600	Enhancers	GM12878-XiMat	blood
30	chr10:52413600-52413800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr10:52413600-52413800	Enhancers	Thymus	Thymus
32	chr10:52413600-52414400	Enhancers	Placenta	Placenta
33	chr10:52413600-52414600	Enhancers	Fetal Muscle Leg	muscle
34	chr10:52413600-52419200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr10:52413600-52419600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:52413600-52419600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links