Variant report

Variant	rs4788579
Chromosome Location	chr16:71951845-71951846
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:71951353-71952199	K562	blood:	n/a	n/a
2	POLR2A	chr16:71951559-71952289	HepG2	liver:	n/a	n/a
3	TAF1	chr16:71951845-71952064	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr16:71951313-71952363	SK-N-SH	brain:	n/a	n/a
5	NFIC	chr16:71951799-71952238	SK-N-SH	brain:	n/a	n/a
6	EP300	chr16:71951835-71952104	SK-N-SH_RA	brain:	n/a	n/a
7	NFIC	chr16:71951325-71952304	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr16:71951300-71952300	SK-N-SH	brain:	n/a	n/a
9	FOSL2	chr16:71951744-71952293	SK-N-SH	brain:	n/a	n/a
10	PBX3	chr16:71951330-71952235	SK-N-SH	brain:	n/a	n/a
11	PBX3	chr16:71951704-71952239	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr16:71951737-71952222	SK-N-SH	brain:	n/a	n/a
13	MAX	chr16:71951783-71952161	SK-N-SH	brain:	n/a	n/a
14	TCF12	chr16:71951344-71952386	SK-N-SH	brain:	n/a	n/a
15	EP300	chr16:71951814-71952071	SK-N-SH_RA	brain:	n/a	n/a
16	GATA3	chr16:71951306-71952390	SK-N-SH	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:71951184..71953960-chr16:72042535..72044526,2	MCF-7	breast:
2	chr16:71931575..71934137-chr16:71950822..71953492,2	MCF-7	breast:
3	chr16:71951326..71953519-chr16:71958185..71960042,2	K562	blood:

No data

Variant related genes	Relation type
IST1	TF binding region
ENSG00000182149	Chromatin interaction
ENSG00000261337	Chromatin interaction
ENSG00000102967	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10500567	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10852505	1.00[CHB][hapmap]
rs11075908	0.92[YRI][hapmap]
rs11075910	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs11639902	1.00[CHB][hapmap]
rs11642529	1.00[CHB][hapmap]
rs11644740	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11648557	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11865456	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12149307	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12149325	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12444594	0.96[EUR][1000 genomes]
rs12444829	0.82[AFR][1000 genomes]
rs12445564	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12445641	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12708918	0.89[EUR][1000 genomes]
rs12708919	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs12934512	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17286411	0.82[ASW][hapmap]
rs17357420	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17358402	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1834036	0.93[EUR][1000 genomes]
rs2288030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2288031	0.89[YRI][hapmap]
rs2878494	1.00[CHB][hapmap]
rs35619990	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751820	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4528577	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4788449	0.92[YRI][hapmap]
rs4788450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4788561	0.87[EUR][1000 genomes]
rs4788566	0.86[YRI][hapmap]
rs4788568	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs4788569	0.90[EUR][1000 genomes]
rs4788575	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs7184486	0.85[YRI][hapmap]
rs7188591	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7195988	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7197486	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7198834	0.85[JPT][hapmap]
rs7202840	1.00[CHB][hapmap]
rs8044004	0.87[EUR][1000 genomes]
rs8044335	0.87[EUR][1000 genomes]
rs8050058	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs8050651	0.88[YRI][hapmap]
rs8051878	1.00[CHB][hapmap]
rs8052358	0.85[JPT][hapmap]
rs8059053	0.82[AFR][1000 genomes]
rs8063324	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs9932707	0.94[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs9939911	0.85[JPT][hapmap]
rs9940234	1.00[CHB][hapmap];0.85[JPT][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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4788579	HP	trans	brain	seeQTL
rs4788579	MTSS1L	cis	parietal	SCAN
rs4788579	TMEM208	cis	parietal	SCAN
rs4788579	AARS	cis	parietal	SCAN
rs4788579	PSMD7	cis	parietal	SCAN
rs4788579	HPR	cis	cerebellum	SCAN
rs4788579	HP	cis	brain	seeQTL
rs4788579	HP	cis	multi-tissue	Pritchard
rs4788579	PDXDC2P	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71931200-71956200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:71937200-71952000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr16:71945200-71959000	Strong transcription	Primary T cells from cord blood	blood
4	chr16:71946000-71956000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr16:71948200-71952800	Strong transcription	Primary B cells from peripheral blood	blood
6	chr16:71948400-71953400	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr16:71948400-71965600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr16:71948600-71952800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr16:71948600-71964000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr16:71948800-71952800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr16:71948800-71953000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr16:71948800-71953200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr16:71948800-71966000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr16:71948800-71966200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr16:71948800-71968800	Strong transcription	Dnd41	blood
16	chr16:71948800-71969600	Strong transcription	Fetal Intestine Large	intestine
17	chr16:71949000-71952200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr16:71949000-71952800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
19	chr16:71949000-71952800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr16:71949000-71964600	Strong transcription	A549	lung
21	chr16:71949000-71966200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr16:71949200-71953000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr16:71949200-71953000	Weak transcription	Brain Angular Gyrus	brain
24	chr16:71949200-71954800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr16:71949200-71956000	Weak transcription	Small Intestine	intestine
26	chr16:71949200-71963000	Strong transcription	K562	blood
27	chr16:71949200-71966600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr16:71949200-71969600	Strong transcription	Fetal Thymus	thymus
29	chr16:71949400-71952800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr16:71949400-71952800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr16:71949400-71956600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr16:71949400-71960000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr16:71949400-71960400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr16:71949400-71963600	Strong transcription	Fetal Kidney	kidney
35	chr16:71949400-71963800	Strong transcription	Fetal Lung	lung
36	chr16:71949400-71965200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr16:71949400-71965800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr16:71949600-71952800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr16:71949600-71952800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr16:71949600-71953000	Strong transcription	NHEK	skin
41	chr16:71949600-71960400	Strong transcription	Placenta	Placenta
42	chr16:71949600-71964800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr16:71949800-71952200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
44	chr16:71949800-71952800	Strong transcription	Primary B cells from cord blood	blood
45	chr16:71949800-71953600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr16:71949800-71954000	Genic enhancers	Adipose Nuclei	Adipose
47	chr16:71949800-71954600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr16:71949800-71960000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr16:71949800-71960600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr16:71949800-71962000	Strong transcription	Sigmoid Colon	Sigmoid Colon

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