Variant report

Variant	rs1879311
Chromosome Location	chr10:43833719-43833720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr10:43833620-43833770	A549	lung:	n/a	n/a
2	CTCF	chr10:43833640-43833790	MCF-7	breast:	n/a	n/a
3	CTCF	chr10:43833580-43833730	RPTEC	kidney:	n/a	n/a
4	CTCF	chr10:43833620-43833770	Caco-2	colon:	n/a	n/a
5	CTCF	chr10:43833640-43833790	Caco-2	colon:	n/a	n/a
6	CTCF	chr10:43833680-43833830	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr10:43833620-43833770	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr10:43833680-43833830	HEK293	kidney:	n/a	n/a
9	CTCF	chr10:43833634-43833848	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr10:43833680-43833830	HBMEC	blood vessel:	n/a	n/a
11	POLR2A	chr10:43833548-43833883	A549	lung:	n/a	n/a
12	CTCF	chr10:43833522-43833797	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr10:43833700-43833850	HBMEC	blood vessel:	n/a	n/a
14	MAX	chr10:43833518-43834191	A549	lung:	n/a	n/a
15	MAX	chr10:43833564-43834007	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr10:43833700-43833850	WERI-Rb-1	eye:	n/a	n/a
17	CTCF	chr10:43833660-43833810	GM12865	blood:	n/a	n/a
18	CTCF	chr10:43833620-43833770	HCT-116	colon:	n/a	n/a
19	MYC	chr10:43833708-43833821	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr10:43833700-43833850	HEEpiC	esophagus:	n/a	n/a
21	CTCF	chr10:43833640-43833790	WERI-Rb-1	eye:	n/a	n/a
22	CTCF	chr10:43833620-43833770	BE2_C	brain:	n/a	n/a
23	ZNF143	chr10:43833603-43833877	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr10:43833700-43833850	HepG2	liver:	n/a	n/a
25	E2F6	chr10:43833558-43833950	H1-hESC	embryonic stem cell:	n/a	n/a
26	E2F6	chr10:43833628-43833894	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr10:43833620-43833770	GM12864	blood:	n/a	n/a
28	CTCF	chr10:43833620-43833770	RPTEC	kidney:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:43832614..43835578-chr10:43888340..43890232,2	MCF-7	breast:
2	chr10:43832495..43835214-chr10:43835530..43838072,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6ATAC11P	TF binding region
ENSG00000221468	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1106215	1.00[ASN][1000 genomes]
rs11238575	1.00[ASN][1000 genomes]
rs17153601	1.00[ASN][1000 genomes]
rs17366781	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856400	1.00[ASN][1000 genomes]
rs2248807	1.00[ASN][1000 genomes]
rs2253260	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264603	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2265955	1.00[ASN][1000 genomes]
rs2819025	1.00[ASN][1000 genomes]
rs2999222	1.00[ASN][1000 genomes]
rs3006393	1.00[ASN][1000 genomes]
rs3006410	1.00[ASN][1000 genomes]
rs3124211	1.00[ASN][1000 genomes]
rs4948727	1.00[ASN][1000 genomes]
rs55765722	1.00[ASN][1000 genomes]
rs56037308	1.00[ASN][1000 genomes]
rs56087058	1.00[ASN][1000 genomes]
rs56234785	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56237566	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56252639	1.00[ASN][1000 genomes]
rs56275379	1.00[ASN][1000 genomes]
rs7072967	1.00[ASN][1000 genomes]
rs7073345	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7084621	1.00[ASN][1000 genomes]
rs7085670	1.00[ASN][1000 genomes]
rs72785234	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785236	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785237	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785243	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785246	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785248	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785255	1.00[ASN][1000 genomes]
rs72785256	1.00[ASN][1000 genomes]
rs72785266	1.00[ASN][1000 genomes]
rs72787434	1.00[ASN][1000 genomes]
rs7916718	1.00[ASN][1000 genomes]

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	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	92 gene(s)	inside rSNPs	diseases
2	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1035873	chr10:43721143-43873664	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv466882	chr10:43721481-43849358	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv550697	chr10:43721481-43849358	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1044422	chr10:43731521-43860307	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43828800-43839600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr10:43828800-43839800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr10:43829000-43834200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr10:43832200-43834000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr10:43832200-43834000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:43832600-43833800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr10:43832600-43833800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr10:43833200-43834000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:43833400-43833800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr10:43833400-43833800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr10:43833400-43834400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr10:43833400-43834600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr10:43833400-43835200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:43833400-43836800	Enhancers	Placenta	Placenta
15	chr10:43833600-43834000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr10:43833600-43834000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:43833600-43834000	Enhancers	Fetal Intestine Large	intestine
18	chr10:43833600-43834000	Flanking Active TSS	A549	lung
19	chr10:43833600-43834200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
20	chr10:43833600-43834400	Enhancers	Pancreas	Pancrea
21	chr10:43833600-43835000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
22	chr10:43833600-43835200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr10:43833600-43835200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr10:43833600-43835200	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr10:43833600-43835200	Enhancers	Lung	lung
26	chr10:43833600-43836600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr10:43833600-43836600	Enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links