Variant report

Variant	rs3751820
Chromosome Location	chr16:71961906-71961907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr16:71961096-71961989	SK-N-SH	brain:	n/a	chr16:71961467-71961475 chr16:71961468-71961475 chr16:71961466-71961476 chr16:71961467-71961475 chr16:71961466-71961476
2	POLR2A	chr16:71961823-71962214	K562	blood:	n/a	n/a
3	POLR2A	chr16:71961851-71962199	GM12878	blood:	n/a	n/a
4	POLR2A	chr16:71961883-71962211	K562	blood:	n/a	n/a
5	POLR2A	chr16:71961702-71962865	GM12892	blood:	n/a	n/a
6	POLR2A	chr16:71961733-71962677	K562	blood:	n/a	n/a
7	POLR2A	chr16:71961886-71962425	GM12891	blood:	n/a	n/a
8	POLR2A	chr16:71961897-71962535	GM12891	blood:	n/a	n/a
9	POLR2A	chr16:71961165-71961953	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr16:71961477-71962008	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr16:71961884-71962404	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr16:71961874-71962342	GM12892	blood:	n/a	n/a
13	POLR2A	chr16:71961766-71962408	GM12892	blood:	n/a	n/a
14	POLR2A	chr16:71961874-71962121	GM12878	blood:	n/a	n/a
15	POLR2A	chr16:71961297-71963359	GM12878	blood:	n/a	n/a
16	POLR2A	chr16:71961473-71969841	K562	blood:	n/a	n/a
17	POLR2A	chr16:71961504-71966488	HepG2	liver:	n/a	n/a
18	POLR2A	chr16:71961634-71962045	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr16:71961450-71963673	GM12878	blood:	n/a	n/a
20	TCF12	chr16:71961107-71962045	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:71934291..71936556-chr16:71961330..71962978,2	MCF-7	breast:
2	chr16:71916310..71918495-chr16:71961448..71964132,2	K562	blood:
3	chr16:71840314..71841978-chr16:71961721..71963575,2	K562	blood:
4	chr16:71954747..71956951-chr16:71960006..71962533,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263320	TF binding region
ENSG00000261337	TF binding region
ENSG00000182149	Chromatin interaction
ENSG00000102984	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10500567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10852505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap]
rs10852507	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11075906	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11075909	0.87[YRI][hapmap]
rs11075910	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11639843	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11640135	0.91[EUR][1000 genomes]
rs11642529	1.00[CHB][hapmap]
rs11644740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11648557	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11861296	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs11865456	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12149307	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12149325	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12149460	0.82[JPT][hapmap]
rs12149917	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12445564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12445641	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12448086	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12708919	1.00[CHB][hapmap]
rs12921279	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12921459	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12927691	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12928939	0.82[GIH][hapmap]
rs12934512	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13330178	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs17357420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs17358402	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288030	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2878494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3088285	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34029919	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34101687	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34664834	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35028754	0.91[EUR][1000 genomes]
rs35209006	0.90[EUR][1000 genomes]
rs35377660	0.85[EUR][1000 genomes]
rs35404791	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35535529	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35595148	0.88[EUR][1000 genomes]
rs36182990	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4528577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4788568	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4788575	0.85[JPT][hapmap]
rs4788579	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs71384781	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71384782	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71386939	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71386940	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71386942	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7185027	0.81[EUR][1000 genomes]
rs7187418	0.87[YRI][hapmap]
rs7188591	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7191848	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7195988	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7197486	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7198834	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7202840	1.00[CHB][hapmap];0.82[GIH][hapmap]
rs73586164	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8046044	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs8049508	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8050058	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8051878	1.00[CHB][hapmap]
rs8052358	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs8053906	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs8054602	0.87[YRI][hapmap]
rs8063657	0.88[EUR][1000 genomes]
rs9939404	0.87[YRI][hapmap]
rs9939911	1.00[JPT][hapmap]
rs9940234	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3751820	PHLPP2	cis	cerebellum	SCAN
rs3751820	PHLPP2	cis	lymphoblastoid	seeQTL
rs3751820	TMEM208	cis	parietal	SCAN
rs3751820	TK2	cis	parietal	SCAN

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	chr16:71948600-71964000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
3	chr16:71948800-71966000	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr16:71948800-71966200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr16:71948800-71968800	Strong transcription	Dnd41	blood
6	chr16:71948800-71969600	Strong transcription	Fetal Intestine Large	intestine
7	chr16:71949000-71964600	Strong transcription	A549	lung
8	chr16:71949000-71966200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr16:71949200-71963000	Strong transcription	K562	blood
10	chr16:71949200-71966600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr16:71949200-71969600	Strong transcription	Fetal Thymus	thymus
12	chr16:71949400-71963600	Strong transcription	Fetal Kidney	kidney
13	chr16:71949400-71963800	Strong transcription	Fetal Lung	lung
14	chr16:71949400-71965200	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr16:71949400-71965800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr16:71949600-71964800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr16:71949800-71962000	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr16:71949800-71963600	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr16:71950000-71964800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr16:71950200-71963400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
21	chr16:71950200-71964200	Strong transcription	Brain Germinal Matrix	brain
22	chr16:71950600-71964800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr16:71950600-71965400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr16:71950600-71969600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr16:71950800-71968800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr16:71951400-71962000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
27	chr16:71951800-71962600	Strong transcription	Pancreas	Pancrea
28	chr16:71951800-71963200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr16:71952600-71964800	Strong transcription	Fetal Brain Female	brain
30	chr16:71953200-71965000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr16:71953200-71965400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr16:71953200-71969600	Strong transcription	Liver	Liver
33	chr16:71953400-71964800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr16:71953800-71965600	Strong transcription	Thymus	Thymus
35	chr16:71953800-71966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr16:71953800-71969000	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr16:71953800-71969600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr16:71954000-71965200	Strong transcription	Primary B cells from cord blood	blood
39	chr16:71954000-71969000	Strong transcription	GM12878-XiMat	blood
40	chr16:71954000-71969000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr16:71954000-71969400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr16:71954000-71969600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr16:71954200-71968200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr16:71954200-71969800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr16:71955000-71969000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr16:71955200-71964600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr16:71956800-71971000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr16:71957800-71963800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr16:71957800-71964000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr16:71958000-71969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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