Variant report

Variant	rs16968998
Chromosome Location	chr15:77897197-77897198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77862030..77863568-chr15:77895689..77897664,2	MCF-7	breast:
2	chr15:77890507..77893828-chr15:77894009..77899298,4	MCF-7	breast:
3	chr15:77896964..77898473-chr15:77923112..77926055,2	K562	blood:

Variant related genes	Relation type
ENSG00000169783	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1104815	0.94[CEU][hapmap]
rs11630235	0.94[CEU][hapmap]
rs11631894	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11633811	0.81[CEU][hapmap]
rs11636780	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638351	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638674	0.94[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16968999	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28368579	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477219	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706124	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3144	0.82[GIH][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap]
rs4286073	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886882	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886884	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4886885	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4886886	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4886887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886888	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171141	0.87[EUR][1000 genomes]
rs8039399	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs884527	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9806139	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv904415	chr15:77845959-77943935	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904416	chr15:77845959-77967416	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv904417	chr15:77851535-77935992	Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904418	chr15:77851535-77963887	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1036749	chr15:77884026-77912408	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv904419	chr15:77897197-77943935	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs16968998	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs16968998	CHRNA5	cis	parietal	SCAN
rs16968998	HMG20A	cis	parietal	SCAN
rs16968998	CHRNA5	cis	cerebellum	SCAN
rs16968998	CYP1A2	cis	cerebellum	SCAN
rs16968998	STRA6	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77891000-77898800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr15:77892200-77897200	Weak transcription	Gastric	stomach
3	chr15:77892200-77897600	Weak transcription	Right Ventricle	heart
4	chr15:77892800-77897200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:77893200-77897200	Weak transcription	K562	blood
6	chr15:77895000-77898600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:77895800-77899800	Enhancers	Fetal Heart	heart
8	chr15:77895800-77901200	Enhancers	Fetal Muscle Leg	muscle
9	chr15:77896000-77897200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:77896000-77897200	Enhancers	Fetal Brain Male	brain
11	chr15:77896200-77897800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr15:77896200-77897800	Enhancers	Fetal Lung	lung
13	chr15:77896200-77898000	Enhancers	Fetal Stomach	stomach
14	chr15:77896200-77900400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr15:77896200-77900600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:77896400-77897200	Enhancers	Fetal Kidney	kidney
17	chr15:77896400-77897400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr15:77896400-77897400	Enhancers	Placenta	Placenta
19	chr15:77896400-77898800	Weak transcription	Left Ventricle	heart
20	chr15:77896400-77900200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:77896600-77897200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr15:77896600-77897200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr15:77896600-77897200	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr15:77896600-77897200	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr15:77896600-77897200	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr15:77896600-77897200	Active TSS	Brain Substantia Nigra	brain
27	chr15:77896600-77897200	ZNF genes & repeats	Spleen	Spleen
28	chr15:77896600-77897400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
29	chr15:77896600-77897400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr15:77896600-77897600	Flanking Active TSS	Fetal Brain Female	brain
31	chr15:77896600-77898200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr15:77896600-77901400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:77896800-77897200	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:77896800-77897200	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr15:77896800-77897200	Active TSS	Brain Germinal Matrix	brain
36	chr15:77896800-77897200	Enhancers	Fetal Muscle Trunk	muscle
37	chr15:77896800-77898800	Enhancers	Lung	lung
38	chr15:77896800-77899400	Enhancers	Colonic Mucosa	Colon
39	chr15:77896800-77899600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:77896800-77899800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:77896800-77901600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:77897000-77897200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:77897000-77897200	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:77897000-77897200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:77897000-77897200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
46	chr15:77897000-77897200	Active TSS	Stomach Smooth Muscle	stomach
47	chr15:77897000-77897400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr15:77897000-77897400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:77897000-77897400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:77897000-77897400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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