Variant report

Variant	rs9940865
Chromosome Location	chr16:82168019-82168020
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10514531	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10514533	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1056629	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs1056654	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs1056690	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11150443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11150444	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11150445	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11641082	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11641178	0.93[EUR][1000 genomes]
rs11642247	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11642251	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11642280	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11642453	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11643324	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs11643724	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11644183	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11645618	0.92[EUR][1000 genomes]
rs11646480	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11647519	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11647563	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11647691	1.00[CEU][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11647928	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11649427	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12444846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12445764	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12446030	0.99[EUR][1000 genomes]
rs12446104	0.99[EUR][1000 genomes]
rs12447225	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12447597	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12447673	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12447876	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12447913	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12448665	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12448672	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12448785	0.95[EUR][1000 genomes]
rs12597638	0.91[CEU][hapmap]
rs12599196	0.91[CEU][hapmap]
rs12931886	0.91[CEU][hapmap]
rs13330853	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13333365	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16956483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16956524	0.99[EUR][1000 genomes]
rs16956527	0.99[EUR][1000 genomes]
rs16956533	0.98[EUR][1000 genomes]
rs16956547	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs16956550	0.98[EUR][1000 genomes]
rs16956555	0.98[EUR][1000 genomes]
rs16956556	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs16956565	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16956572	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs16956576	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs17804513	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17804602	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862821	0.82[CEU][hapmap]
rs2081256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2081257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2081258	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2098749	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2098750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303268	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs2911428	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs35328670	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3751863	0.97[EUR][1000 genomes]
rs3751865	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs3794705	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3829542	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs3829552	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs4243231	0.82[CEU][hapmap]
rs4530129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4569272	0.82[CEU][hapmap]
rs4888206	0.99[EUR][1000 genomes]
rs4888207	0.99[EUR][1000 genomes]
rs4889463	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4889465	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4889468	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4889475	0.99[EUR][1000 genomes]
rs4889478	0.87[EUR][1000 genomes]
rs4889480	0.86[EUR][1000 genomes]
rs61366082	1.00[EUR][1000 genomes]
rs7186965	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7187080	0.91[CEU][hapmap]
rs7193463	0.91[CEU][hapmap]
rs7193586	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7195778	0.91[CEU][hapmap];0.86[TSI][hapmap]
rs72487977	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73591443	0.81[ASN][1000 genomes]
rs7404586	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7498125	0.91[CEU][hapmap]
rs7501253	0.91[CEU][hapmap]
rs9922715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929117	0.91[CEU][hapmap]
rs9929380	0.91[CEU][hapmap]
rs9936872	0.91[CEU][hapmap]
rs9937667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940821	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9941179	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532598	chr16:82034475-82738733	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv532599	chr16:82074439-82926863	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv457578	chr16:82136566-82197883	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv573366	chr16:82136566-82197883	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking 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
5	nsv573367	chr16:82140561-83040846	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv457579	chr16:82150293-82216622	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv573368	chr16:82150293-82216622	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv907013	chr16:82154619-82196808	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv525467	chr16:82154619-82223485	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv457580	chr16:82165183-82182104	Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv573369	chr16:82165183-82182104	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv573370	chr16:82165183-82185320	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1061064	chr16:82165314-82213799	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv1056381	chr16:82165314-82215388	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1062687	chr16:82165516-82213799	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9940865	MPHOSPH6	cis	lymphoblastoid	seeQTL
rs9940865	HSBP1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:82157000-82191200	Weak transcription	Fetal Brain Male	brain
2	chr16:82160200-82172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr16:82160800-82170600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr16:82160800-82171600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr16:82160800-82171600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr16:82160800-82172200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr16:82160800-82172200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr16:82161000-82172000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr16:82161000-82172000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr16:82161200-82170200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr16:82164000-82169000	Weak transcription	HepG2	liver
12	chr16:82164200-82179400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr16:82165800-82179200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr16:82166000-82172200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr16:82166600-82168200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr16:82166600-82172800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr16:82167000-82168600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr16:82167000-82168600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr16:82167200-82168200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr16:82167200-82168400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr16:82167200-82168400	Flanking Active TSS	Dnd41	blood
22	chr16:82167200-82168600	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr16:82167200-82168800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr16:82167200-82170200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr16:82167200-82179200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr16:82167400-82179400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr16:82167600-82168400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr16:82167600-82170600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr16:82167600-82172200	Weak transcription	Esophagus	oesophagus
30	chr16:82167600-82180600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr16:82167800-82171000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr16:82167800-82172000	Weak transcription	Fetal Thymus	thymus
33	chr16:82167800-82180200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr16:82168000-82168400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr16:82168000-82168600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr16:82168000-82168600	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr16:82168000-82168800	Enhancers	Primary T cells from cord blood	blood
38	chr16:82168000-82168800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr16:82168000-82170200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr16:82168000-82172400	Weak transcription	Thymus	Thymus
41	chr16:82168000-82181000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr16:82168000-82195400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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