Variant report

Variant	rs510398
Chromosome Location	chr11:66054823-66054824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66053955-66057415	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr11:66053948-66057304	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr11:66054531-66054835	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:66054822-66055167	MCF-7	breast:	n/a	n/a
5	POLR2A	chr11:66054040-66060816	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr11:66054255-66055058	K562	blood:	n/a	n/a
7	HCFC1	chr11:66054469-66058486	Hela-S3	cervix:	n/a	n/a
8	SPI1	chr11:66054776-66055639	HL-60	blood:	n/a	chr11:66055400-66055407
9	POLR2A	chr11:66054796-66057408	K562	blood:	n/a	n/a
10	POLR2A	chr11:66054763-66055401	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr11:66054135-66055044	HepG2	liver:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65987811..65990997-chr11:66051307..66054931,3	MCF-7	breast:
2	chr11:66053947..66059144-chr11:66077550..66083439,18	K562	blood:
3	chr11:66023140..66025945-chr11:66052736..66056629,3	MCF-7	breast:
4	chr11:66054499..66057435-chr11:66115136..66117035,2	MCF-7	breast:
5	chr11:66054488..66057665-chr11:66080176..66082833,4	K562	blood:
6	chr11:66053447..66056540-chr11:66100445..66105768,7	MCF-7	breast:
7	chr11:66054433..66056920-chr11:66384363..66386136,2	K562	blood:
8	chr11:66052361..66057023-chr11:66137906..66140994,4	MCF-7	breast:
9	chr11:66025864..66027446-chr11:66054760..66056847,2	MCF-7	breast:
10	chr11:66041439..66043181-chr11:66053492..66056458,2	MCF-7	breast:
11	chr11:66054404..66057808-chr11:66078165..66081775,4	MCF-7	breast:
12	chr11:66054162..66056937-chr11:66109546..66111530,2	K562	blood:
13	chr11:65625599..65627439-chr11:66053239..66055711,2	K562	blood:
14	chr11:66034858..66038328-chr11:66053749..66060447,9	MCF-7	breast:
15	chr11:66054081..66055900-chr11:66092894..66095581,2	MCF-7	breast:

No data

Variant related genes	Relation type
YIF1A	TF binding region
TMEM151A	TF binding region
ENSG00000175115	Chromatin interaction
ENSG00000174903	Chromatin interaction
ENSG00000174996	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000254762	Chromatin interaction
ENSG00000174744	Chromatin interaction
ENSG00000174684	Chromatin interaction
ENSG00000254458	Chromatin interaction
ENSG00000174669	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000174791	Chromatin interaction
ENSG00000254756	Chromatin interaction
ENSG00000255468	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1151532	0.85[AFR][1000 genomes]
rs1190945	0.92[AFR][1000 genomes]
rs1190946	0.86[AFR][1000 genomes]
rs1203551	0.92[AFR][1000 genomes]
rs1203552	0.92[AFR][1000 genomes]
rs1203749	0.85[AFR][1000 genomes]
rs1203750	0.85[AFR][1000 genomes]
rs1203801	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1630638	0.81[AFR][1000 genomes]
rs1783732	1.00[YRI][hapmap]
rs2452687	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs3016315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3017606	0.89[AFR][1000 genomes]
rs471203	1.00[MEX][hapmap]
rs471709	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs472853	0.85[AFR][1000 genomes]
rs475817	0.85[AFR][1000 genomes]
rs477001	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs504456	0.85[AFR][1000 genomes]
rs505412	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs505642	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs512316	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs515778	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs519911	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs527279	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs541954	1.00[YRI][hapmap]
rs547282	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs547892	0.85[AFR][1000 genomes]
rs549228	0.85[AFR][1000 genomes]
rs551652	0.85[AFR][1000 genomes]
rs555527	1.00[YRI][hapmap]
rs555826	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs559298	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs560105	0.85[AFR][1000 genomes]
rs561199	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs561869	0.85[AFR][1000 genomes]
rs567414	0.85[AFR][1000 genomes]
rs568423	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs571368	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs572697	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs577301	0.85[AFR][1000 genomes]
rs581247	0.92[AFR][1000 genomes]
rs693382	0.85[AFR][1000 genomes]
rs7947668	0.81[AFR][1000 genomes]
rs948358	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv897773	chr11:66041807-66063654	Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv555223	chr11:66041807-66064126	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv897774	chr11:66042962-66063654	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv897775	chr11:66042962-66064850	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv897776	chr11:66042962-66066349	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv897777	chr11:66044882-66063654	Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv897778	chr11:66044882-66066349	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv897779	chr11:66047523-66063654	Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	34 gene(s)	inside rSNPs	diseases
14	esv3350047	chr11:66054759-66055124	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs510398	LOC404266	trans	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66042000-66055600	Weak transcription	Fetal Kidney	kidney
2	chr11:66047400-66055400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:66050400-66055000	Weak transcription	Left Ventricle	heart
4	chr11:66050400-66055200	Weak transcription	Fetal Heart	heart
5	chr11:66050400-66055400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr11:66050400-66055400	Weak transcription	Psoas Muscle	Psoas
7	chr11:66050600-66055000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr11:66050600-66055200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:66050600-66055200	Strong transcription	NHLF	lung
10	chr11:66050600-66055400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:66050600-66055400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:66050600-66055600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:66050800-66055000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:66050800-66055200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:66050800-66055200	Weak transcription	Primary B cells from cord blood	blood
16	chr11:66050800-66055200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:66050800-66055200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr11:66050800-66055200	Weak transcription	Hela-S3	cervix
19	chr11:66050800-66055400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:66050800-66055400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr11:66051000-66055400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr11:66051000-66055400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:66051000-66055400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr11:66051800-66055000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:66051800-66055200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:66052000-66055200	Strong transcription	NHEK	skin
27	chr11:66052200-66055400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:66052600-66055200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
29	chr11:66052800-66055400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:66053000-66055200	Weak transcription	HMEC	breast
31	chr11:66053000-66055400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:66053200-66055400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:66053400-66055000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:66053400-66055000	Strong transcription	Fetal Brain Female	brain
35	chr11:66053400-66055000	Weak transcription	Ovary	ovary
36	chr11:66053400-66055200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr11:66053400-66055200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:66053400-66055200	Weak transcription	Fetal Lung	lung
39	chr11:66053400-66055200	Genic enhancers	Stomach Smooth Muscle	stomach
40	chr11:66053400-66055200	Weak transcription	A549	lung
41	chr11:66053600-66055000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr11:66053600-66055200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr11:66053600-66055200	Weak transcription	Primary T cells from cord blood	blood
44	chr11:66053600-66055200	Weak transcription	Right Ventricle	heart
45	chr11:66053600-66055200	Weak transcription	NHDF-Ad	bronchial
46	chr11:66053600-66055400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:66053600-66055400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr11:66053600-66055400	Enhancers	Liver	Liver
49	chr11:66053600-66055400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr11:66053800-66055200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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