Variant report

Variant	rs12447968
Chromosome Location	chr16:74897248-74897249
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:74742978..74743967-chr16:74896355..74897696,20	MCF-7	breast:
2	chr16:74846665..74847640-chr16:74896133..74897263,15	MCF-7	breast:
3	chr16:74743044..74743998-chr16:74896217..74897613,10	K562	blood:
4	chr16:74895557..74898464-chr16:74921092..74923999,2	MCF-7	breast:
5	chr16:74896697..74898617-chr16:75031619..75033637,2	MCF-7	breast:
6	chr16:74846723..74847755-chr16:74896368..74897323,9	K562	blood:
7	chr16:74743023..74743972-chr16:74896115..74897278,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186187	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1024503	1.00[ASN][1000 genomes]
rs10514386	1.00[ASN][1000 genomes]
rs11645307	1.00[ASN][1000 genomes]
rs11863300	1.00[ASN][1000 genomes]
rs11864313	1.00[ASN][1000 genomes]
rs11864349	1.00[ASN][1000 genomes]
rs11866550	1.00[ASN][1000 genomes]
rs12444462	1.00[ASN][1000 genomes]
rs12444618	1.00[ASN][1000 genomes]
rs12445200	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12446147	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12919626	1.00[ASN][1000 genomes]
rs12921263	1.00[ASN][1000 genomes]
rs14308	0.80[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16950254	1.00[ASW][hapmap]
rs28810133	1.00[ASN][1000 genomes]
rs34130324	1.00[ASN][1000 genomes]
rs34393456	1.00[ASN][1000 genomes]
rs34398985	1.00[ASN][1000 genomes]
rs34937987	1.00[ASN][1000 genomes]
rs34992867	1.00[ASN][1000 genomes]
rs35038783	1.00[ASN][1000 genomes]
rs35173843	1.00[ASN][1000 genomes]
rs35195349	1.00[ASN][1000 genomes]
rs35456018	1.00[ASN][1000 genomes]
rs35937344	1.00[ASN][1000 genomes]
rs4887788	1.00[ASN][1000 genomes]
rs4888281	1.00[ASN][1000 genomes]
rs4888307	1.00[ASN][1000 genomes]
rs4985359	1.00[ASN][1000 genomes]
rs55727944	1.00[ASN][1000 genomes]
rs55836977	1.00[ASN][1000 genomes]
rs55859029	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56009261	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56313952	1.00[ASN][1000 genomes]
rs58303079	1.00[ASN][1000 genomes]
rs62052860	1.00[ASN][1000 genomes]
rs62052861	1.00[ASN][1000 genomes]
rs71392613	1.00[ASN][1000 genomes]
rs71392614	1.00[ASN][1000 genomes]
rs71392615	1.00[ASN][1000 genomes]
rs7203228	1.00[ASN][1000 genomes]
rs72794783	1.00[ASN][1000 genomes]
rs72796668	1.00[ASN][1000 genomes]
rs72796671	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72796672	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72796678	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72796696	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72798603	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72798608	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72798613	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72798621	1.00[ASN][1000 genomes]
rs72798647	1.00[ASN][1000 genomes]
rs72798648	1.00[ASN][1000 genomes]
rs72798683	1.00[ASN][1000 genomes]
rs72798700	1.00[ASN][1000 genomes]
rs74024559	1.00[ASN][1000 genomes]
rs74024565	1.00[ASN][1000 genomes]
rs8047659	1.00[ASN][1000 genomes]
rs8062012	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9937139	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
3	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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	111 gene(s)	inside rSNPs	diseases
4	nsv1058900	chr16:74753819-75005050	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv542958	chr16:74753819-75005050	Weak transcription Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	esv3345041	chr16:74756263-75066969	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
7	nsv457520	chr16:74758984-74907440	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv572976	chr16:74758984-74907440	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv431516	chr16:74840166-75099566	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
11	nsv833280	chr16:74855811-75077227	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv1059764	chr16:74868327-74989488	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1064546	chr16:74868795-74989488	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv572977	chr16:74873513-74954897	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv526213	chr16:74873513-74990061	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv572978	chr16:74873574-74990004	Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv1063842	chr16:74896749-74990601	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv542959	chr16:74896749-74990601	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12447968	ADAT1	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74884000-74905600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:74896600-74898800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr16:74896800-74899800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:74896800-74900000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr16:74896800-74900000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr16:74896800-74903200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr16:74896800-74905400	Weak transcription	Liver	Liver
8	chr16:74896800-74905600	Weak transcription	Brain Substantia Nigra	brain
9	chr16:74896800-74907600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr16:74896800-74925200	Weak transcription	Stomach Mucosa	stomach
11	chr16:74897000-74900000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr16:74897000-74900000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr16:74897000-74900000	Weak transcription	Colon Smooth Muscle	Colon
14	chr16:74897000-74900200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr16:74897000-74901200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr16:74897000-74901400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr16:74897000-74904200	Weak transcription	Fetal Intestine Small	intestine
18	chr16:74897000-74905600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr16:74897000-74907600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr16:74897000-74913000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr16:74897000-74917400	Weak transcription	Hela-S3	cervix
22	chr16:74897200-74897600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr16:74897200-74897800	Enhancers	HepG2	liver
24	chr16:74897200-74898400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr16:74897200-74899600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr16:74897200-74900000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr16:74897200-74900000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr16:74897200-74900000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr16:74897200-74900000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr16:74897200-74900200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr16:74897200-74901200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr16:74897200-74905600	Weak transcription	Brain Anterior Caudate	brain
33	chr16:74897200-74907200	Weak transcription	Brain Hippocampus Middle	brain
34	chr16:74897200-74907600	Weak transcription	GM12878-XiMat	blood
35	chr16:74897200-74909000	Weak transcription	A549	lung
36	chr16:74897200-74914400	Weak transcription	K562	blood

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