Variant report

Variant	rs948494
Chromosome Location	chr11:65552118-65552119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65544951..65562337-chr11:65623093..65630859,34	MCF-7	breast:
2	chr11:65549748..65553562-chr11:65663861..65667886,4	K562	blood:
3	chr11:65551696..65553777-chr11:65562013..65564216,2	K562	blood:
4	chr11:65545624..65552162-chr11:65622017..65629334,15	K562	blood:
5	chr11:65551999..65553570-chr11:65651722..65654050,2	K562	blood:
6	chr11:65338114..65341460-chr11:65551554..65554469,3	MCF-7	breast:
7	chr11:65549963..65553451-chr11:65657304..65660070,4	K562	blood:
8	chr11:65415695..65418870-chr11:65549508..65552161,3	MCF-7	breast:
9	chr11:65479523..65484500-chr11:65551483..65556601,5	MCF-7	breast:
10	chr11:65381741..65384368-chr11:65551453..65554074,4	MCF-7	breast:
11	chr11:65545830..65548787-chr11:65550897..65553141,2	K562	blood:
12	chr11:65549046..65552132-chr11:65553796..65556282,6	K562	blood:
13	chr11:65551697..65554555-chr11:65655334..65658299,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000265874	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000172818	Chromatin interaction
ENSG00000175827	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000213445	Chromatin interaction
ENSG00000173465	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000254470	Chromatin interaction
ENSG00000176973	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1074155	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap]
rs1074156	0.92[CEU][hapmap];0.81[CHB][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap]
rs10896032	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs10896037	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896038	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11227279	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11227281	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11227299	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11532071	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11537193	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11600918	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11604451	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11604462	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11604568	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11606947	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12225620	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12289836	0.87[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap]
rs1466462	0.81[CHB][hapmap]
rs4014192	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4014195	0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4645927	0.92[CEU][hapmap];0.81[CHD][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap]
rs4645933	0.86[ASW][hapmap];0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap]
rs479844	0.83[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs4930312	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4930313	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4930319	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56686587	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6591188	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs7110576	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7115734	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs7123489	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs746429	0.85[MEX][hapmap]
rs7947604	0.92[CEU][hapmap]
rs948493	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9666878	0.92[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
2	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
3	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
4	nsv897758	chr11:65490756-65564035	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv897759	chr11:65543827-65554502	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
6	nsv897760	chr11:65545306-65559266	Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs948494	SIPA1	cis	cerebellum	SCAN
rs948494	DKFZp761E198	cis	lymphoblastoid	seeQTL
rs948494	RNASEH2C	cis	parietal	SCAN
rs948494	PCNXL3	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65548600-65553400	Weak transcription	Gastric	stomach
2	chr11:65549000-65553000	Enhancers	Placenta	Placenta
3	chr11:65549200-65552200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:65549200-65552200	Enhancers	HMEC	breast
5	chr11:65549200-65552600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr11:65549200-65552600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:65549200-65554200	Weak transcription	Right Atrium	heart
8	chr11:65549400-65552600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:65549400-65553000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:65549600-65552200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr11:65549600-65552400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:65549600-65552600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr11:65549600-65552800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr11:65549600-65553000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr11:65549600-65553400	Weak transcription	Colonic Mucosa	Colon
16	chr11:65549600-65553400	Weak transcription	Pancreas	Pancrea
17	chr11:65549800-65552800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:65550800-65552800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:65550800-65553200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:65551200-65553400	Bivalent Enhancer	Thymus	Thymus
21	chr11:65551200-65555600	Bivalent Enhancer	Fetal Thymus	thymus
22	chr11:65551400-65552200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:65551400-65552200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
24	chr11:65551400-65552200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr11:65551400-65553400	Enhancers	Esophagus	oesophagus
26	chr11:65551600-65552200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
27	chr11:65551600-65552400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:65551600-65552400	Strong transcription	Fetal Intestine Small	intestine
29	chr11:65551800-65552200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
30	chr11:65552000-65552200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
31	chr11:65552000-65552200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:65552000-65552400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr11:65552000-65552600	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr11:65552000-65552600	Bivalent Enhancer	HepG2	liver
35	chr11:65552000-65553800	Weak transcription	NHEK	skin

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