Variant report

Variant	rs9859822
Chromosome Location	chr3:195166449-195166450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr3:195166406-195167076	K562	blood:	n/a	n/a
2	PML	chr3:195166400-195167049	K562	blood:	n/a	n/a
3	POLR2A	chr3:195166417-195166992	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:195164614..195167496-chr3:195169106..195172382,4	K562	blood:
2	chr3:195162578..195166480-chr3:195268710..195271525,3	K562	blood:
3	chr3:194892527..194894676-chr3:195164792..195166496,2	K562	blood:
4	chr3:195164614..195167502-chr3:195169044..195171295,4	K562	blood:
5	chr3:194980181..194984046-chr3:195161738..195167079,6	K562	blood:
6	chr3:195163742..195165509-chr3:195165685..195167332,2	K562	blood:
7	chr3:195162962..195165336-chr3:195165436..195167180,2	MCF-7	breast:

No data

Variant related genes	Relation type
ACAP2	TF binding region
ENSG00000223711	Chromatin interaction
ENSG00000114331	Chromatin interaction
ENSG00000173950	Chromatin interaction
ENSG00000184203	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10933704	1.00[CHB][hapmap]
rs12630162	0.91[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs13317782	0.83[ASN][1000 genomes]
rs1353133	0.83[ASN][1000 genomes]
rs1890853	1.00[CHB][hapmap];0.81[GIH][hapmap];0.81[ASN][1000 genomes]
rs2000052	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs2029708	1.00[CHB][hapmap];0.82[GIH][hapmap]
rs2050806	1.00[CHB][hapmap];0.82[GIH][hapmap]
rs2131685	0.82[ASN][1000 genomes]
rs2410792	0.83[ASN][1000 genomes]
rs4677666	1.00[CHB][hapmap]
rs4677828	0.82[GIH][hapmap]
rs4677839	1.00[CHB][hapmap];0.82[GIH][hapmap];0.81[ASN][1000 genomes]
rs4677840	1.00[CHB][hapmap]
rs4677844	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs55636917	0.99[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs58067895	0.81[ASN][1000 genomes]
rs62288444	0.91[EUR][1000 genomes]
rs6437376	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6763588	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs6785382	0.83[ASN][1000 genomes]
rs6800562	1.00[CHB][hapmap];0.82[GIH][hapmap]
rs6801750	1.00[CHB][hapmap];0.82[GIH][hapmap];0.81[ASN][1000 genomes]
rs7623135	0.81[ASN][1000 genomes]
rs7627671	0.81[ASN][1000 genomes]
rs7635603	0.93[CHB][hapmap];0.82[GIH][hapmap]
rs9288744	1.00[CHB][hapmap];0.82[GIH][hapmap]
rs9288746	1.00[CHB][hapmap];0.82[GIH][hapmap]
rs931528	0.81[GIH][hapmap]
rs9814214	1.00[CHB][hapmap];0.84[GIH][hapmap];0.82[ASN][1000 genomes]
rs9840309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs9844354	1.00[CHB][hapmap]
rs9847544	1.00[CHB][hapmap]
rs9864603	1.00[CHB][hapmap]
rs9868768	0.81[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	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
2	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
3	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
4	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
6	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
7	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
9	nsv432512	chr3:195007260-195475989	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
10	nsv878138	chr3:195057001-195477791	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
11	nsv1006229	chr3:195071421-195474751	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
12	esv2754364	chr3:195102703-195553690	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
13	esv2757028	chr3:195102787-195479748	Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
14	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers 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 miRNA target site	144 gene(s)	inside rSNPs	diseases
15	nsv432513	chr3:195121072-195478861	Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
16	nsv432514	chr3:195121110-195478861	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
17	nsv432515	chr3:195121110-195528226	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
18	nsv829824	chr3:195131067-195286698	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9859822	BCOR	trans	cerebellum	SCAN
rs9859822	XXYLT1	cis	Esophagus Mucosa	GTEx
rs9859822	TEX14	trans	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195163800-195166600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:195164600-195166600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:195164600-195166600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:195164600-195166800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:195164600-195166800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:195164600-195167200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:195164600-195170800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:195164600-195171000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:195164600-195171200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:195164800-195166600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:195164800-195166600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:195164800-195166600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:195164800-195166800	Weak transcription	Primary B cells from cord blood	blood
14	chr3:195164800-195166800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:195164800-195166800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:195164800-195167000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:195164800-195167000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:195164800-195167000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:195164800-195167000	Weak transcription	Stomach Mucosa	stomach
20	chr3:195164800-195167200	Weak transcription	Fetal Intestine Large	intestine
21	chr3:195164800-195167400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr3:195164800-195167800	Weak transcription	Fetal Intestine Small	intestine
23	chr3:195165000-195166800	Weak transcription	Fetal Thymus	thymus
24	chr3:195165000-195166800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:195165000-195167200	Enhancers	Primary T cells from cord blood	blood
26	chr3:195165200-195166800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:195165200-195166800	Weak transcription	HepG2	liver
28	chr3:195165200-195167000	Weak transcription	K562	blood
29	chr3:195165400-195166600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr3:195165400-195166800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr3:195165400-195166800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:195165400-195166800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:195165600-195166600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:195165600-195166800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:195166400-195167400	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr3:195166400-195167400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr3:195166400-195167400	Enhancers	GM12878-XiMat	blood

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