Variant report

Variant	rs11880356
Chromosome Location	chr19:42827541-42827542
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:42827527-42827582	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr19:42827460-42828092	H1-hESC	embryonic stem cell:	n/a	n/a
3	USF1	chr19:42827524-42828005	H1-hESC	embryonic stem cell:	n/a	chr19:42827969-42827985 chr19:42827713-42827729
4	MAX	chr19:42827437-42828802	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr19:42827384-42828021	H1-hESC	embryonic stem cell:	n/a	chr19:42827974-42827984
6	E2F6	chr19:42827425-42828098	H1-hESC	embryonic stem cell:	n/a	chr19:42827974-42827984

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:42805228..42807979-chr19:42827043..42829586,2	K562	blood:
2	chr19:42819448..42823717-chr19:42824551..42827641,3	MCF-7	breast:
3	chr19:42826137..42828658-chr19:42828732..42831619,2	K562	blood:
4	chr19:42757670..42761057-chr19:42823055..42828263,5	K562	blood:
5	chr19:42612431..42613391-chr19:42826906..42827875,2	MCF-7	breast:
6	chr19:42820314..42825247-chr19:42826529..42830814,5	K562	blood:
7	chr19:42806459..42808702-chr19:42827247..42830028,2	K562	blood:
8	chr19:42787475..42788198-chr19:42826786..42827551,2	K562	blood:

No data

Variant related genes	Relation type
MEGF8	TF binding region
ENSG00000268643	Chromatin interaction
ENSG00000188368	Chromatin interaction
ENSG00000079432	Chromatin interaction
ENSG00000105722	Chromatin interaction
ENSG00000079462	Chromatin interaction
ENSG00000105429	Chromatin interaction
ENSG00000167619	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10401224	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10402438	1.00[EUR][1000 genomes]
rs10403856	1.00[AMR][1000 genomes]
rs10404650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10406800	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs10406972	1.00[EUR][1000 genomes]
rs10407085	1.00[EUR][1000 genomes]
rs10407155	1.00[EUR][1000 genomes]
rs10407842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408258	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10409428	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10409433	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10409939	1.00[EUR][1000 genomes]
rs10410129	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10410174	1.00[AMR][1000 genomes]
rs10410653	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411498	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10413484	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414056	0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs10414695	1.00[AMR][1000 genomes]
rs10415478	0.85[YRI][hapmap]
rs10415759	1.00[AMR][1000 genomes]
rs10415999	1.00[EUR][1000 genomes]
rs10416241	0.85[YRI][hapmap]
rs10416535	0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418102	1.00[AMR][1000 genomes]
rs10418312	0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420327	1.00[AMR][1000 genomes]
rs10421026	0.84[AFR][1000 genomes]
rs10421331	1.00[AMR][1000 genomes]
rs10421409	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421510	0.93[YRI][hapmap];1.00[EUR][1000 genomes]
rs10421857	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421902	1.00[AMR][1000 genomes]
rs10422301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10422867	1.00[EUR][1000 genomes]
rs10423812	1.00[EUR][1000 genomes]
rs10423959	1.00[EUR][1000 genomes]
rs10423978	1.00[EUR][1000 genomes]
rs10424402	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10425003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10425320	1.00[EUR][1000 genomes]
rs10425783	1.00[EUR][1000 genomes]
rs10426267	1.00[EUR][1000 genomes]
rs10426284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878207	0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11878297	1.00[EUR][1000 genomes]
rs11879073	1.00[EUR][1000 genomes]
rs11879538	1.00[EUR][1000 genomes]
rs11880214	1.00[EUR][1000 genomes]
rs11882107	1.00[EUR][1000 genomes]
rs11882801	1.00[EUR][1000 genomes]
rs12165130	1.00[EUR][1000 genomes]
rs13343322	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13343966	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13345986	0.81[AFR][1000 genomes]
rs13346831	1.00[AMR][1000 genomes]
rs13346837	1.00[EUR][1000 genomes]
rs13346879	1.00[AMR][1000 genomes]
rs2229614	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28402882	1.00[AMR][1000 genomes]
rs28463673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28469564	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28474957	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28483598	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28496975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28532592	0.81[AFR][1000 genomes]
rs28572784	0.85[YRI][hapmap]
rs28657829	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28663042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28675019	1.00[EUR][1000 genomes]
rs28675764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28686771	1.00[AMR][1000 genomes]
rs28699037	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28711448	1.00[EUR][1000 genomes]
rs28715574	1.00[EUR][1000 genomes]
rs33919763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35707383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36089262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41407146	1.00[AMR][1000 genomes]
rs59870753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60950516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6509012	0.81[AFR][1000 genomes]
rs7246232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248473	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7254853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7255343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258727	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73552879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73554520	1.00[EUR][1000 genomes]
rs73554531	1.00[EUR][1000 genomes]
rs73558432	1.00[AMR][1000 genomes]
rs73560411	1.00[AMR][1000 genomes]
rs8099885	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109258	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9304602	0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription 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	70 gene(s)	inside rSNPs	diseases
6	nsv833834	chr19:42736444-42835027	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	42 gene(s)	inside rSNPs	diseases
7	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42818000-42828600	Weak transcription	Right Atrium	heart
2	chr19:42818200-42828600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr19:42818200-42828800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:42818200-42829200	Weak transcription	Gastric	stomach
5	chr19:42818400-42828800	Weak transcription	Brain Angular Gyrus	brain
6	chr19:42818800-42828800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr19:42819000-42828400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:42821600-42829200	Weak transcription	K562	blood
9	chr19:42827400-42827600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
10	chr19:42827400-42827600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
11	chr19:42827400-42827600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
12	chr19:42827400-42827600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
13	chr19:42827400-42827600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
14	chr19:42827400-42827600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:42827400-42827600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:42827400-42827600	Bivalent/Poised TSS	Thymus	Thymus
17	chr19:42827400-42827800	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr19:42827400-42828000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:42827400-42829200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr19:42827400-42829400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr19:42827400-42830800	Active TSS	H9 Cell Line	embryonic stem cell

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