Variant report

Variant	rs1706816
Chromosome Location	chr15:45460422-45460423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:45460420-45460570	GM12872	blood:	n/a	n/a
2	MAZ	chr15:45458538-45460756	IMR90	lung:	n/a	chr15:45459166-45459182 chr15:45460742-45460751
3	POLR2A	chr15:45460409-45460424	K562	blood:	n/a	n/a
4	CTCF	chr15:45460380-45460530	GM12875	blood:	n/a	n/a
5	POLR2A	chr15:45456690-45460622	HepG2	liver:	n/a	n/a
6	CTCF	chr15:45458854-45460599	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr15:45460266-45460725	GM12878	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45459427..45462384-chr15:45693635..45696116,3	K562	blood:
2	chr15:45459774..45461695-chr15:45467150..45468709,2	K562	blood:
3	chr15:45458146..45462463-chr15:45465556..45468797,6	MCF-7	breast:
4	chr15:45458222..45460718-chr15:45477355..45481212,4	K562	blood:
5	chr15:45459519..45461778-chr15:45469004..45470564,2	K562	blood:
6	chr15:45458776..45462841-chr15:45467209..45473486,10	K562	blood:
7	chr15:45457275..45460718-chr15:45477484..45481344,4	K562	blood:
8	chr15:45459071..45462844-chr15:45693635..45696532,4	K562	blood:
9	chr15:45458639..45462602-chr15:45463163..45466877,10	K562	blood:
10	chr15:45458639..45463256-chr15:45489443..45493548,9	K562	blood:
11	chr15:45458882..45460694-chr15:45692968..45695992,3	MCF-7	breast:
12	chr15:45444706..45447350-chr15:45459510..45461724,2	K562	blood:
13	chr15:45457999..45463256-chr15:45488727..45493013,8	K562	blood:
14	chr15:45458782..45460452-chr15:45469150..45471146,2	MCF-7	breast:
15	chr15:45457610..45461525-chr15:45477333..45480560,5	MCF-7	breast:
16	chr15:45457346..45461990-chr15:45488766..45494297,11	MCF-7	breast:
17	chr15:45458064..45460777-chr15:45570184..45573179,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259539	TF binding region
ENSG00000259519	TF binding region
ENSG00000260035	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000171763	Chromatin interaction
ENSG00000259520	Chromatin interaction
ENSG00000137857	Chromatin interaction
ENSG00000259932	Chromatin interaction
ENSG00000138606	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12438755	0.81[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs12899786	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs12908943	0.86[ASN][1000 genomes]
rs1648305	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1648306	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1648309	0.99[ASN][1000 genomes]
rs16939752	1.00[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs16939774	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs16940351	0.90[CEU][hapmap];0.85[TSI][hapmap]
rs16941238	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs1706778	0.86[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs1706818	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271436	0.86[EUR][1000 genomes]
rs2292467	0.86[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs2467821	0.88[ASN][1000 genomes]
rs2467825	0.88[ASN][1000 genomes]
rs28375309	0.83[EUR][1000 genomes]
rs3784584	0.87[EUR][1000 genomes]
rs56294809	0.96[EUR][1000 genomes]
rs60001836	0.88[ASN][1000 genomes]
rs7173906	0.86[EUR][1000 genomes]
rs7174075	0.86[EUR][1000 genomes]
rs7174412	0.86[EUR][1000 genomes]
rs7182081	0.83[EUR][1000 genomes]
rs7182508	0.86[EUR][1000 genomes]
rs74011381	0.81[EUR][1000 genomes]
rs74011382	0.96[EUR][1000 genomes]
rs8038802	0.86[EUR][1000 genomes]
rs8040896	0.86[ASN][1000 genomes]

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	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv457124	chr15:45381998-45460422	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv569312	chr15:45381998-45460422	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv518213	chr15:45421758-45464768	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
11	esv3323980	chr15:45458085-45460633	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1706816	TP53BP1	cis	parietal	SCAN
rs1706816	RPAP1	cis	cerebellum	SCAN
rs1706816	B2M	cis	cerebellum	SCAN
rs1706816	SLC30A4	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45458800-45460600	Active TSS	Duodenum Mucosa	Duodenum
2	chr15:45459600-45461200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:45459600-45461800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:45459600-45463800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:45459600-45469200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:45459800-45460600	Flanking Active TSS	Hela-S3	cervix
7	chr15:45459800-45461200	Enhancers	Gastric	stomach
8	chr15:45459800-45461200	Enhancers	Pancreas	Pancrea
9	chr15:45459800-45461800	Enhancers	Spleen	Spleen
10	chr15:45459800-45462200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:45459800-45462400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr15:45459800-45462400	Enhancers	Primary B cells from peripheral blood	blood
13	chr15:45459800-45463200	Weak transcription	Ovary	ovary
14	chr15:45459800-45471800	Weak transcription	Small Intestine	intestine
15	chr15:45459800-45478000	Weak transcription	Aorta	Aorta
16	chr15:45460000-45460600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:45460000-45460600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:45460000-45460600	Enhancers	Esophagus	oesophagus
19	chr15:45460000-45460600	Enhancers	Placenta	Placenta
20	chr15:45460000-45460600	Enhancers	Fetal Thymus	thymus
21	chr15:45460000-45460600	Enhancers	Left Ventricle	heart
22	chr15:45460000-45461000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr15:45460000-45461200	Enhancers	Fetal Brain Male	brain
24	chr15:45460000-45461200	Weak transcription	Right Atrium	heart
25	chr15:45460000-45461600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr15:45460000-45461800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:45460000-45461800	Weak transcription	GM12878-XiMat	blood
28	chr15:45460000-45462000	Weak transcription	Primary B cells from cord blood	blood
29	chr15:45460000-45462000	Weak transcription	HSMM	muscle
30	chr15:45460000-45462200	Enhancers	Brain Hippocampus Middle	brain
31	chr15:45460000-45462400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr15:45460000-45462400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:45460000-45462400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:45460000-45462400	Enhancers	Primary hematopoietic stem cells	blood
35	chr15:45460000-45462400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr15:45460000-45462600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr15:45460000-45463800	Weak transcription	Right Ventricle	heart
38	chr15:45460000-45465000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:45460000-45465600	Weak transcription	Fetal Intestine Large	intestine
40	chr15:45460000-45465600	Weak transcription	HSMMtube	muscle
41	chr15:45460000-45466600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:45460000-45471600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:45460000-45471800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr15:45460000-45472200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:45460000-45474800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:45460000-45477200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr15:45460000-45478600	Weak transcription	Thymus	Thymus
48	chr15:45460200-45460600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:45460200-45460600	Enhancers	Adipose Nuclei	Adipose
50	chr15:45460200-45460600	Enhancers	Brain Anterior Caudate	brain

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