Variant report

Variant	rs11642386
Chromosome Location	chr16:12184064-12184065
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12174212..12176270-chr16:12182353..12184871,2	K562	blood:
2	chr16:12183674..12186424-chr16:12186757..12189168,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261293	Chromatin interaction
ENSG00000241641	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11075049	0.94[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs11075054	0.80[ASN][1000 genomes]
rs11639701	0.93[ASN][1000 genomes]
rs11642033	0.85[ASN][1000 genomes]
rs11646458	0.89[ASN][1000 genomes]
rs11646539	0.80[ASN][1000 genomes]
rs11646584	0.85[ASN][1000 genomes]
rs11647572	0.81[ASN][1000 genomes]
rs11648228	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11648468	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11648816	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12596549	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12596703	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12599090	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12599793	0.80[ASN][1000 genomes]
rs12708746	0.81[ASN][1000 genomes]
rs12708747	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12926900	0.81[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];0.98[ASN][1000 genomes]
rs12929519	0.85[ASN][1000 genomes]
rs13333662	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs13336687	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16958964	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2175020	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2457193	0.85[ASN][1000 genomes]
rs28439695	0.86[ASN][1000 genomes]
rs28667047	0.85[ASN][1000 genomes]
rs2869808	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs350233	0.82[JPT][hapmap]
rs350264	0.85[ASN][1000 genomes]
rs350265	0.81[ASN][1000 genomes]
rs350266	0.81[ASN][1000 genomes]
rs35053871	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35318501	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35542345	0.85[ASN][1000 genomes]
rs3851011	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851012	0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[ASN][1000 genomes]
rs3894905	0.88[JPT][hapmap];0.85[MEX][hapmap]
rs4780411	0.97[ASN][1000 genomes]
rs4781180	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs71385189	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7200307	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8048589	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8050180	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs8055516	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8059989	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8062015	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8063329	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9925009	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9935284	0.80[ASN][1000 genomes]
rs9939383	0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv977111	chr16:12161129-12220593	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1039492	chr16:12176517-12210702	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv571460	chr16:12181702-12238602	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11642386	TNFRSF17	cis	cerebellum	SCAN
rs11642386	TNFRSF17	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12142800-12189200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr16:12156000-12185800	Weak transcription	Brain Germinal Matrix	brain
3	chr16:12156000-12185800	Weak transcription	Fetal Brain Female	brain
4	chr16:12157200-12185800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:12157800-12185800	Weak transcription	HSMMtube	muscle
6	chr16:12167600-12185800	Weak transcription	HSMM	muscle
7	chr16:12175200-12185000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr16:12178600-12199600	Weak transcription	Aorta	Aorta
9	chr16:12181600-12184200	Enhancers	Placenta	Placenta
10	chr16:12181600-12184400	Enhancers	Primary B cells from cord blood	blood
11	chr16:12181600-12184400	Enhancers	Esophagus	oesophagus
12	chr16:12181800-12184400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr16:12181800-12184400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr16:12182200-12188600	Weak transcription	Fetal Brain Male	brain
15	chr16:12182800-12184200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr16:12182800-12184200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr16:12182800-12184400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr16:12183200-12184200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr16:12183200-12184200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr16:12183200-12184200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr16:12183200-12184200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr16:12183200-12184200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr16:12183200-12184200	Flanking Active TSS	Thymus	Thymus
24	chr16:12183200-12184400	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr16:12183200-12184400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr16:12183200-12184600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr16:12183200-12184600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr16:12183200-12186200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr16:12183400-12184200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
30	chr16:12183400-12184200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr16:12183400-12184200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr16:12183400-12184200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr16:12183400-12184200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr16:12183400-12184200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr16:12183400-12184200	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr16:12183400-12184200	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr16:12183400-12184200	Flanking Active TSS	Fetal Muscle Trunk	muscle
38	chr16:12183400-12184200	Flanking Active TSS	Fetal Thymus	thymus
39	chr16:12183400-12184200	Enhancers	Gastric	stomach
40	chr16:12183400-12184200	Flanking Active TSS	Left Ventricle	heart
41	chr16:12183400-12184200	Flanking Active TSS	HUVEC	blood vessel
42	chr16:12183400-12184200	Flanking Active TSS	NHEK	skin
43	chr16:12183400-12184400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr16:12183400-12184400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr16:12183400-12184400	Enhancers	Lung	lung
46	chr16:12183400-12184400	Enhancers	Spleen	Spleen
47	chr16:12183400-12184600	Enhancers	HepG2	liver
48	chr16:12183600-12184200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr16:12183600-12184200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr16:12183600-12184200	Flanking Active TSS	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links