Variant report

Variant	rs16973500
Chromosome Location	chr16:71965196-71965197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71945578..71947499-chr16:71964859..71966489,2	MCF-7	breast:
2	chr16:71927384..71929645-chr16:71963039..71965792,3	MCF-7	breast:
3	chr16:71927209..71930992-chr16:71962077..71965220,3	K562	blood:
4	chr16:71955110..71958047-chr16:71963028..71965520,2	MCF-7	breast:
5	chr16:71927209..71930992-chr16:71962077..71965660,4	K562	blood:

Variant related genes	Relation type
ENSG00000102984	Chromatin interaction
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10492825	0.84[CHB][hapmap]
rs1049794	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12919947	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12921355	0.84[CHB][hapmap]
rs12926408	0.86[ASN][1000 genomes]
rs12930036	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1549292	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16973477	0.91[CEU][hapmap];0.81[CHD][hapmap];0.94[LWK][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes]
rs16973520	0.84[CHB][hapmap];0.91[GIH][hapmap]
rs2878491	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34235351	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3794691	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57807129	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57949916	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61523290	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72801786	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72801789	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72801797	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8053891	0.89[CHB][hapmap]
rs8055242	0.84[CHB][hapmap]
rs952159	0.85[CHB][hapmap]
rs952160	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs9925462	0.89[CHB][hapmap];0.84[GIH][hapmap]
rs9928413	0.89[CHB][hapmap];0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv906893	chr16:71922663-71988728	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
Attention deficit hyperactivity disorder and conduct disorder	18951430	GWAS catalog

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71948400-71965600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr16:71948800-71966000	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr16:71948800-71966200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:71948800-71968800	Strong transcription	Dnd41	blood
5	chr16:71948800-71969600	Strong transcription	Fetal Intestine Large	intestine
6	chr16:71949000-71966200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr16:71949200-71966600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr16:71949200-71969600	Strong transcription	Fetal Thymus	thymus
9	chr16:71949400-71965200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr16:71949400-71965800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr16:71950600-71965400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr16:71950600-71969600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr16:71950800-71968800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr16:71953200-71965400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr16:71953200-71969600	Strong transcription	Liver	Liver
16	chr16:71953800-71965600	Strong transcription	Thymus	Thymus
17	chr16:71953800-71966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr16:71953800-71969000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr16:71953800-71969600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr16:71954000-71965200	Strong transcription	Primary B cells from cord blood	blood
21	chr16:71954000-71969000	Strong transcription	GM12878-XiMat	blood
22	chr16:71954000-71969000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr16:71954000-71969400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr16:71954000-71969600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr16:71954200-71968200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr16:71954200-71969800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr16:71955000-71969000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr16:71956800-71971000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr16:71958000-71969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr16:71961000-71966000	Strong transcription	Primary T cells from cord blood	blood
31	chr16:71961200-71966400	Strong transcription	HepG2	liver
32	chr16:71961600-71965200	Weak transcription	Stomach Mucosa	stomach
33	chr16:71961600-71965400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr16:71961800-71969600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr16:71962000-71971200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr16:71962400-71967800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr16:71962600-71967600	Weak transcription	Colonic Mucosa	Colon
38	chr16:71962600-71967800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr16:71962600-71967800	Weak transcription	Aorta	Aorta
40	chr16:71962600-71967800	Weak transcription	Pancreas	Pancrea
41	chr16:71962600-71969600	Strong transcription	Placenta	Placenta
42	chr16:71962600-71972000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr16:71963000-71967600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr16:71963200-71966200	Weak transcription	Spleen	Spleen
45	chr16:71963200-71966400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr16:71963200-71967800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr16:71963200-71967800	Weak transcription	Gastric	stomach
48	chr16:71963200-71967800	Weak transcription	Lung	lung
49	chr16:71963200-71968400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr16:71963200-71972000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links