Variant report

Variant	rs4898494
Chromosome Location	chrX:153654122-153654123
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chrX:153653796-153654141	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chrX:153653660-153654354	A549	lung:	n/a	n/a
3	CTCF	chrX:153654020-153654170	RPTEC	kidney:	n/a	n/a
4	ZNF384	chrX:153653766-153654339	K562	blood:	n/a	n/a
5	CTCF	chrX:153654060-153654210	BE2_C	brain:	n/a	n/a
6	CTCF	chrX:153653703-153654138	K562	blood:	n/a	n/a
7	CTCF	chrX:153654040-153654190	HCM	heart:	n/a	n/a
8	POLR2A	chrX:153653886-153654532	K562	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chrX:153600528..153603480-chrX:153653809..153656728,2	MCF-7	breast:
2	chrX:153651973..153654173-chrX:153766111..153768679,2	K562	blood:
3	chrX:153650030..153651762-chrX:153652711..153655102,2	MCF-7	breast:
4	chrX:153639768..153641812-chrX:153653862..153655651,2	MCF-7	breast:
5	chrX:153652971..153655441-chrX:153681410..153682985,2	K562	blood:
6	chrX:153652659..153655089-chrX:153713536..153716056,2	MCF-7	breast:
7	chrX:153649493..153652025-chrX:153653871..153656499,2	K562	blood:
8	X:153614328-153625659..X:153649561-153657611	Hela-S3	cervix:
9	chrX:153624019..153633071-chrX:153652023..153663795,26	MCF-7	breast:
10	X:153649561-153657611..X:153719993-153730954	Hela-S3	cervix:
11	chrX:153647321..153649991-chrX:153651614..153655245,3	MCF-7	breast:
12	chrX:153596552..153604370-chrX:153654056..153661278,16	MCF-7	breast:
13	chrX:153652480..153655334-chrX:153762320..153764290,2	K562	blood:
14	chrX:153637503..153641560-chrX:153652741..153657919,6	K562	blood:

No data

Variant related genes	Relation type
ATP6AP1	TF binding region
ENSG00000264783	Chromatin interaction
ENSG00000264631	Chromatin interaction
ENSG00000264484	Chromatin interaction
ENSG00000196924	Chromatin interaction
ENSG00000160211	Chromatin interaction
ENSG00000102125	Chromatin interaction
ENSG00000207165	Chromatin interaction
ENSG00000147403	Chromatin interaction
ENSG00000013563	Chromatin interaction
ENSG00000102178	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1130929	1.00[JPT][hapmap]
rs11593	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs12559	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12877	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2051508	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2070643	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs2070807	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2070819	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2070821	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2070825	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2070827	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2070829	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2097214	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2156911	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs2239469	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2283762	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs28602900	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4898484	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs743547	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs743548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs743549	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs762514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs7886627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs915941	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs915942	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531227	chrX:152864376-153655730	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
2	esv33199	chrX:152864376-153820241	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	276 gene(s)	inside rSNPs	diseases
3	nsv528291	chrX:152864376-153827637	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	277 gene(s)	inside rSNPs	diseases
4	nsv915605	chrX:153333946-153783638	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
5	nsv519042	chrX:153348431-153829693	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
6	nsv532962	chrX:153564946-153870337	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	199 gene(s)	inside rSNPs	diseases
7	nsv532963	chrX:153576890-153822717	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	195 gene(s)	inside rSNPs	diseases
8	nsv530281	chrX:153622940-153783184	Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
9	nsv532964	chrX:153622940-153854307	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4898494	PLXNA3	cis	multi-tissue	Pritchard
rs4898494	DNASE1L1	cis	multi-tissue	Pritchard
rs4898494	FAM50A	cis	lymphoblastoid	seeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153640400-153656400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chrX:153640400-153656400	Weak transcription	Small Intestine	intestine
3	chrX:153640600-153656200	Weak transcription	Fetal Kidney	kidney
4	chrX:153640600-153656600	Weak transcription	Aorta	Aorta
5	chrX:153640800-153656600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chrX:153641000-153655600	Weak transcription	Brain Cingulate Gyrus	brain
7	chrX:153641000-153656800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chrX:153641200-153656400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chrX:153641200-153656400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chrX:153641400-153655200	Weak transcription	Duodenum Mucosa	Duodenum
11	chrX:153641400-153655600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chrX:153641400-153655600	Weak transcription	Liver	Liver
13	chrX:153641400-153656200	Weak transcription	Brain Hippocampus Middle	brain
14	chrX:153641400-153656200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chrX:153641400-153656400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chrX:153641400-153656400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chrX:153641400-153656400	Weak transcription	Osteobl	bone
18	chrX:153641600-153655200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chrX:153641600-153655400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chrX:153641600-153655600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chrX:153641600-153655600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chrX:153641600-153656400	Weak transcription	Primary B cells from cord blood	blood
23	chrX:153641600-153656400	Weak transcription	Esophagus	oesophagus
24	chrX:153641800-153655400	Weak transcription	Pancreas	Pancrea
25	chrX:153641800-153656200	Weak transcription	Primary B cells from peripheral blood	blood
26	chrX:153641800-153656200	Weak transcription	A549	lung
27	chrX:153642400-153656200	Weak transcription	Brain Germinal Matrix	brain
28	chrX:153642600-153655400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chrX:153642600-153656200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chrX:153642600-153656400	Weak transcription	Primary T cells from cord blood	blood
31	chrX:153644000-153655400	Weak transcription	Fetal Lung	lung
32	chrX:153644000-153656400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chrX:153648800-153655200	Weak transcription	Brain Angular Gyrus	brain
34	chrX:153649000-153655400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chrX:153649000-153656400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chrX:153649200-153656400	Weak transcription	Right Atrium	heart
37	chrX:153649400-153655400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chrX:153649400-153656200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chrX:153649800-153655400	Weak transcription	Right Ventricle	heart
40	chrX:153649800-153655600	Weak transcription	Fetal Thymus	thymus
41	chrX:153649800-153656400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chrX:153649800-153656400	Weak transcription	Left Ventricle	heart
43	chrX:153650000-153655200	Weak transcription	Adipose Nuclei	Adipose
44	chrX:153650000-153655200	Weak transcription	Ovary	ovary
45	chrX:153650000-153655400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chrX:153650000-153655400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chrX:153650000-153655400	Weak transcription	Gastric	stomach
48	chrX:153650000-153655800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chrX:153650000-153655800	Weak transcription	Spleen	Spleen
50	chrX:153650000-153656200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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