Variant report

Variant	rs3809632
Chromosome Location	chr16:81347389-81347390
allele	C/T
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	RFX5	chr16:81347222-81347498	H1-hESC	embryonic stem cell:	n/a	n/a
2	WRNIP1	chr16:81347364-81347569	GM12878	blood:	n/a	n/a
3	YY1	chr16:81347329-81347678	HepG2	liver:	n/a	n/a
4	GATA3	chr16:81347322-81347811	SH-SY5Y	brain:	n/a	n/a
5	ARID3A	chr16:81347348-81347586	HepG2	liver:	n/a	n/a
6	MYBL2	chr16:81347296-81348886	HepG2	liver:	n/a	n/a
7	POLR2A	chr16:81347117-81348145	H1-hESC	embryonic stem cell:	n/a	n/a
8	ATF2	chr16:81347185-81347717	H1-hESC	embryonic stem cell:	n/a	n/a
9	CEBPB	chr16:81347329-81347705	H1-hESC	embryonic stem cell:	n/a	n/a
10	TEAD4	chr16:81347110-81347707	H1-hESC	embryonic stem cell:	n/a	chr16:81347498-81347507
11	SP1	chr16:81347233-81347692	H1-hESC	embryonic stem cell:	n/a	n/a
12	SIN3A	chr16:81347094-81349480	H1-hESC	embryonic stem cell:	n/a	chr16:81349182-81349195 chr16:81349360-81349373
13	POLR2A	chr16:81347074-81348885	H1-hESC	embryonic stem cell:	n/a	n/a
14	TBP	chr16:81347136-81347747	H1-hESC	embryonic stem cell:	n/a	n/a
15	BACH1	chr16:81347131-81347730	H1-hESC	embryonic stem cell:	n/a	n/a
16	ATF2	chr16:81347128-81347709	H1-hESC	embryonic stem cell:	n/a	n/a
17	TEAD4	chr16:81347204-81347682	K562	blood:	n/a	chr16:81347498-81347507
18	SIN3AK20	chr16:81347289-81349895	MCF-7	breast:	n/a	n/a
19	SIN3AK20	chr16:81347183-81347740	H1-hESC	embryonic stem cell:	n/a	n/a
20	MXI1	chr16:81346949-81350033	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr16:81346947-81349653	H1-hESC	embryonic stem cell:	n/a	n/a
22	TCF12	chr16:81347325-81347548	H1-hESC	embryonic stem cell:	n/a	chr16:81347398-81347406
23	YY1	chr16:81347213-81348048	H1-hESC	embryonic stem cell:	n/a	chr16:81347788-81347797
24	CHD1	chr16:81347036-81348799	H1-hESC	embryonic stem cell:	n/a	chr16:81348543-81348550
25	RCOR1	chr16:81347380-81350098	IMR90	lung:	n/a	n/a
26	TCF12	chr16:81347234-81347530	H1-hESC	embryonic stem cell:	n/a	chr16:81347398-81347406
27	TAF1	chr16:81347161-81347687	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr16:81347318-81347682	H1-hESC	embryonic stem cell:	n/a	n/a
29	SP1	chr16:81347067-81347700	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr16:81347307-81347675	K562	blood:	n/a	n/a
31	POLR2A	chr16:81347361-81347591	ProgFib	skin:	n/a	n/a
32	MYC	chr16:81347248-81347744	H1-hESC	embryonic stem cell:	n/a	n/a
33	GTF2F1	chr16:81347302-81347645	H1-hESC	embryonic stem cell:	n/a	n/a
34	EGR1	chr16:81347379-81348775	MCF-7	breast:	n/a	chr16:81348498-81348511 chr16:81347790-81347800 chr16:81347790-81347800 chr16:81348500-81348510 chr16:81348498-81348511 chr16:81347790-81347801 chr16:81347783-81347796 chr16:81348501-81348510 chr16:81348497-81348512 chr16:81347789-81347802 chr16:81348500-81348510 chr16:81347786-81347800 chr16:81348470-81348484 chr16:81348498-81348511 chr16:81348498-81348512 chr16:81348498-81348511 chr16:81347789-81347799 chr16:81348494-81348516 chr16:81347787-81347797 chr16:81347789-81347802 chr16:81347788-81347802 chr16:81347788-81347803 chr16:81348499-81348510 chr16:81347790-81347799 chr16:81347539-81347563 chr16:81347784-81347806 chr16:81347789-81347802 chr16:81347789-81347802
35	CTCF	chr16:81347240-81347390	HCPEpiC	choroid plexus:	n/a	n/a
36	POLR2A	chr16:81347347-81347716	HepG2	liver:	n/a	n/a
37	YY1	chr16:81347386-81347629	K562	blood:	n/a	n/a
38	POLR2A	chr16:81347088-81348915	H1-hESC	embryonic stem cell:	n/a	n/a
39	TEAD4	chr16:81347015-81347772	H1-hESC	embryonic stem cell:	n/a	chr16:81347498-81347507
40	YY1	chr16:81347141-81347744	H1-hESC	embryonic stem cell:	n/a	n/a
41	TAF1	chr16:81347042-81348902	H1-hESC	embryonic stem cell:	n/a	n/a
42	CHD2	chr16:81347112-81347649	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAX	chr16:81347219-81347790	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAX	chr16:81347254-81347768	H1-hESC	embryonic stem cell:	n/a	n/a
45	GATA3	chr16:81347324-81347874	MCF-7	breast:	n/a	n/a
46	REST	chr16:81347127-81349140	H1-neurons	neurons:	n/a	chr16:81348978-81348991 chr16:81348122-81348130
47	POLR2A	chr16:81347099-81347727	H1-hESC	embryonic stem cell:	n/a	n/a
48	TEAD4	chr16:81347068-81347800	HepG2	liver:	n/a	chr16:81347498-81347507
49	JUND	chr16:81347190-81347691	H1-hESC	embryonic stem cell:	n/a	n/a
50	ESRRA	chr16:81347218-81348857	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:81109518..81111024-chr16:81347327..81349963,2	K562	blood:
2	chr16:81038258..81040784-chr16:81347032..81349945,2	K562	blood:
3	chr16:81038653..81041025-chr16:81346635..81349129,2	MCF-7	breast:
4	chr16:81110316..81112473-chr16:81346981..81348533,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GCSH-1	chr16:81345111-81348378	NONHSAT143942

Variant related genes	Relation type
ENSG00000260495	TF binding region
GAN	TF binding region
ENSG00000245059	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000166455	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10454708	0.95[ASN][1000 genomes]
rs11150384	0.95[ASN][1000 genomes]
rs11150385	1.00[CEU][hapmap]
rs11150386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11865151	1.00[MEX][hapmap]
rs12149852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12597517	0.82[ASN][1000 genomes]
rs12599564	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12924233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16954797	1.00[MEX][hapmap]
rs2059281	1.00[CEU][hapmap]
rs2925978	1.00[MEX][hapmap]
rs3809633	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4468614	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4522413	0.89[ASN][1000 genomes]
rs4598907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[ASN][1000 genomes]
rs4888135	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4888137	0.89[ASN][1000 genomes]
rs4888138	1.00[CEU][hapmap]
rs4889299	1.00[JPT][hapmap]
rs6564868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7184259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7186648	0.95[ASN][1000 genomes]
rs7195134	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7196075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7203686	1.00[CEU][hapmap]
rs8055879	0.89[ASN][1000 genomes]
rs8060840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9925582	1.00[MEX][hapmap]
rs9926795	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9928668	1.00[MEX][hapmap]
rs9934395	1.00[CEU][hapmap]
rs9940292	0.95[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	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers 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 miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
5	nsv522890	chr16:81341363-81348396	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81338400-81347400	Weak transcription	Aorta	Aorta
2	chr16:81338600-81347400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr16:81343200-81347400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr16:81345000-81347400	Weak transcription	Lung	lung
5	chr16:81345400-81347400	Weak transcription	Left Ventricle	heart
6	chr16:81345800-81347400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr16:81346400-81347400	Enhancers	Primary T cells fromperipheralblood	blood
8	chr16:81346400-81347400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr16:81346400-81347400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr16:81346400-81347400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr16:81346400-81347400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr16:81346400-81347400	Enhancers	Fetal Stomach	stomach
13	chr16:81346400-81347600	Enhancers	Primary B cells from peripheral blood	blood
14	chr16:81346400-81347600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr16:81346600-81347600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr16:81346600-81347600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr16:81346600-81347600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr16:81346600-81347600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr16:81346600-81349400	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr16:81346800-81348600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr16:81346800-81349400	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr16:81346800-81349400	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr16:81346800-81349800	Active TSS	H1 Cell Line	embryonic stem cell
24	chr16:81346800-81350200	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr16:81347000-81347400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr16:81347000-81347400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr16:81347000-81347400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr16:81347000-81347400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr16:81347000-81347400	Enhancers	Adipose Nuclei	Adipose
30	chr16:81347000-81347400	Enhancers	Fetal Kidney	kidney
31	chr16:81347000-81347400	Enhancers	Fetal Muscle Leg	muscle
32	chr16:81347000-81347400	Enhancers	Ovary	ovary
33	chr16:81347000-81347400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr16:81347000-81347400	Enhancers	Psoas Muscle	Psoas
35	chr16:81347000-81347400	Enhancers	Right Atrium	heart
36	chr16:81347000-81347400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr16:81347000-81347400	Enhancers	Thymus	Thymus
38	chr16:81347000-81347600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr16:81347000-81347600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr16:81347000-81347600	Enhancers	Liver	Liver
41	chr16:81347000-81347600	Enhancers	Fetal Heart	heart
42	chr16:81347000-81347600	Enhancers	Right Ventricle	heart
43	chr16:81347000-81347600	Flanking Active TSS	HepG2	liver
44	chr16:81347000-81347800	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr16:81347000-81347800	Flanking Active TSS	Fetal Brain Male	brain
46	chr16:81347000-81347800	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr16:81347000-81347800	Enhancers	Small Intestine	intestine
48	chr16:81347000-81347800	Enhancers	Spleen	Spleen
49	chr16:81347000-81347800	Flanking Active TSS	GM12878-XiMat	blood
50	chr16:81347000-81348000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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