Variant report

Variant	rs1530895
Chromosome Location	chr16:46954348-46954349
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr16:46954279-46954950	ECC-1	luminal epithelium:	n/a	chr16:46954589-46954605 chr16:46954588-46954605
2	NR2F2	chr16:46954279-46954834	MCF-7	breast:	n/a	n/a
3	POLR2A	chr16:46954010-46954566	HepG2	liver:	n/a	n/a
4	FOSL2	chr16:46952698-46954399	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:46954156-46954659	HL-60	blood:	n/a	n/a
6	POLR2A	chr16:46951422-46955022	HepG2	liver:	n/a	n/a
7	SP1	chr16:46954294-46954908	HCT-116	colon:	n/a	n/a
8	GATA3	chr16:46954323-46954871	MCF-7	breast:	n/a	n/a
9	NFIC	chr16:46954285-46954937	ECC-1	luminal epithelium:	n/a	chr16:46954589-46954605 chr16:46954588-46954605
10	POLR2A	chr16:46951155-46967607	HepG2	liver:	n/a	n/a
11	POLR2A	chr16:46952647-46955036	HepG2	liver:	n/a	n/a
12	POLR2A	chr16:46953781-46954637	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr16:46951891-46955073	HepG2	liver:	n/a	n/a
14	TCF7L2	chr16:46954348-46954883	MCF-7	breast:	n/a	chr16:46954614-46954630 chr16:46954615-46954629 chr16:46954614-46954630 chr16:46954618-46954627

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:46916414..46917983-chr16:46954082..46956744,2	K562	blood:
2	chr16:46953985..46956976-chr16:46957030..46958598,2	K562	blood:

Variant related genes	Relation type
GPT2	TF binding region
ENSG00000166123	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10902629	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11860636	1.00[AMR][1000 genomes]
rs12598707	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1466170	1.00[AMR][1000 genomes]
rs1542292	1.00[AMR][1000 genomes]
rs1641120	1.00[AMR][1000 genomes]
rs1645939	1.00[AMR][1000 genomes]
rs1651658	1.00[AMR][1000 genomes]
rs1651659	1.00[AMR][1000 genomes]
rs166096	1.00[AMR][1000 genomes]
rs168745	1.00[AMR][1000 genomes]
rs1698957	1.00[AMR][1000 genomes]
rs185213	1.00[AMR][1000 genomes]
rs1865837	1.00[AMR][1000 genomes]
rs1865838	1.00[AMR][1000 genomes]
rs194054	1.00[AMR][1000 genomes]
rs194055	1.00[AMR][1000 genomes]
rs1992075	1.00[AMR][1000 genomes]
rs1992078	1.00[AMR][1000 genomes]
rs2034599	1.00[AMR][1000 genomes]
rs250420	1.00[AMR][1000 genomes]
rs250421	1.00[AMR][1000 genomes]
rs252723	1.00[AMR][1000 genomes]
rs252724	1.00[AMR][1000 genomes]
rs252725	1.00[AMR][1000 genomes]
rs252727	1.00[AMR][1000 genomes]
rs252728	1.00[AMR][1000 genomes]
rs252732	1.00[AMR][1000 genomes]
rs252733	1.00[AMR][1000 genomes]
rs252734	1.00[AMR][1000 genomes]
rs28185	1.00[AMR][1000 genomes]
rs36309	1.00[AMR][1000 genomes]
rs36311	1.00[AMR][1000 genomes]
rs36313	1.00[AMR][1000 genomes]
rs36314	1.00[AMR][1000 genomes]
rs36317	1.00[AMR][1000 genomes]
rs36459	1.00[AMR][1000 genomes]
rs36461	1.00[AMR][1000 genomes]
rs36463	1.00[AMR][1000 genomes]
rs36465	1.00[AMR][1000 genomes]
rs36466	1.00[AMR][1000 genomes]
rs36467	1.00[AMR][1000 genomes]
rs36470	1.00[AMR][1000 genomes]
rs36473	1.00[AMR][1000 genomes]
rs36474	1.00[AMR][1000 genomes]
rs36475	1.00[AMR][1000 genomes]
rs36477	1.00[AMR][1000 genomes]
rs36482	1.00[AMR][1000 genomes]
rs40164	1.00[AMR][1000 genomes]
rs408906	1.00[AMR][1000 genomes]
rs41232	1.00[AMR][1000 genomes]
rs414928	1.00[AMR][1000 genomes]
rs420560	1.00[AMR][1000 genomes]
rs425556	1.00[AMR][1000 genomes]
rs438275	1.00[AMR][1000 genomes]
rs449778	1.00[AMR][1000 genomes]
rs4966603	1.00[AMR][1000 genomes]
rs4967594	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4967595	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62057622	1.00[AMR][1000 genomes]
rs633699	1.00[AMR][1000 genomes]
rs637583	1.00[AMR][1000 genomes]
rs6598679	1.00[AMR][1000 genomes]
rs6598781	1.00[AMR][1000 genomes]
rs695997	1.00[AMR][1000 genomes]
rs698417	1.00[AMR][1000 genomes]
rs698419	1.00[AMR][1000 genomes]
rs700580	1.00[AMR][1000 genomes]
rs700581	1.00[AMR][1000 genomes]
rs7184436	1.00[AMR][1000 genomes]
rs7192389	1.00[AMR][1000 genomes]
rs794283	1.00[AMR][1000 genomes]
rs794557	1.00[AMR][1000 genomes]
rs794558	1.00[AMR][1000 genomes]
rs794559	1.00[AMR][1000 genomes]
rs797016	1.00[AMR][1000 genomes]
rs8044120	1.00[AMR][1000 genomes]
rs8046818	1.00[AMR][1000 genomes]
rs8047302	1.00[AMR][1000 genomes]
rs8048535	1.00[AMR][1000 genomes]
rs8049238	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs8049734	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs808428	1.00[AMR][1000 genomes]
rs808436	1.00[AMR][1000 genomes]
rs811196	1.00[AMR][1000 genomes]
rs811267	1.00[AMR][1000 genomes]
rs811734	1.00[AMR][1000 genomes]
rs937659	1.00[AMR][1000 genomes]
rs9922581	1.00[AMR][1000 genomes]
rs9930036	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS 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 target site	49 gene(s)	inside rSNPs	diseases
4	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers 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 target site	54 gene(s)	inside rSNPs	diseases
6	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	esv3519767	chr16:46873184-46960035	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	8 gene(s)	inside rSNPs	diseases
8	esv3519768	chr16:46873184-46960035	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv1831215	chr16:46907546-46962858	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv1799095	chr16:46916670-46972671	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1063660	chr16:46930623-46978792	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46919000-46963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:46928400-46966000	Strong transcription	Fetal Brain Female	brain
3	chr16:46929400-46965200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:46930600-46956200	Weak transcription	Fetal Intestine Small	intestine
5	chr16:46930800-46965400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr16:46930800-46968400	Weak transcription	Right Atrium	heart
7	chr16:46931600-46957800	Strong transcription	Fetal Stomach	stomach
8	chr16:46931600-46965200	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr16:46932200-46956200	Weak transcription	Left Ventricle	heart
10	chr16:46932200-46965200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr16:46932400-46957600	Weak transcription	Psoas Muscle	Psoas
12	chr16:46933600-46959800	Weak transcription	HUVEC	blood vessel
13	chr16:46933600-46965400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr16:46933800-46965800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr16:46934000-46963400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr16:46935400-46958200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr16:46936600-46956000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr16:46936600-46956200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr16:46939600-46964800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr16:46940000-46964600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr16:46941200-46955000	Enhancers	Primary B cells from peripheral blood	blood
22	chr16:46942800-46956200	Weak transcription	Colon Smooth Muscle	Colon
23	chr16:46943200-46965200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr16:46943200-46965400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr16:46943400-46954800	Strong transcription	Fetal Muscle Leg	muscle
26	chr16:46943400-46965000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr16:46943400-46965000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr16:46943400-46965200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr16:46943400-46965400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr16:46943400-46965400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr16:46943400-46965400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr16:46943600-46959400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr16:46945200-46957400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr16:46945400-46955000	Strong transcription	Brain Germinal Matrix	brain
35	chr16:46945800-46965200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr16:46945800-46965400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr16:46946000-46955200	Weak transcription	Hela-S3	cervix
38	chr16:46946200-46957800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr16:46948800-46958800	Strong transcription	NHEK	skin
40	chr16:46949200-46955000	Genic enhancers	HepG2	liver
41	chr16:46949200-46963400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
42	chr16:46949400-46956200	Weak transcription	Right Ventricle	heart
43	chr16:46949600-46956000	Weak transcription	NH-A	brain
44	chr16:46949600-46957400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr16:46949800-46957000	Weak transcription	Fetal Intestine Large	intestine
46	chr16:46949800-46957400	Weak transcription	Aorta	Aorta
47	chr16:46949800-46964200	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr16:46950000-46955800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr16:46950000-46956200	Weak transcription	NHLF	lung
50	chr16:46950000-46957400	Weak transcription	Fetal Kidney	kidney

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