Variant report

Variant	rs3829527
Chromosome Location	chr16:12708403-12708404
allele	G/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	MAX	chr16:12706139-12708451	A549	lung:	n/a	n/a
2	POLR2A	chr16:12706361-12708773	HepG2	liver:	n/a	n/a
3	MYBL2	chr16:12706243-12708494	HepG2	liver:	n/a	n/a
4	JUND	chr16:12707113-12708416	K562	blood:	n/a	chr16:12707672-12707683 chr16:12707700-12707711
5	POLR2A	chr16:12706322-12708936	HepG2	liver:	n/a	n/a
6	HEY1	chr16:12706259-12708431	HepG2	liver:	n/a	n/a
7	MAX	chr16:12706171-12708652	HepG2	liver:	n/a	n/a
8	MBD4	chr16:12706264-12708452	HepG2	liver:	n/a	n/a
9	POLR2A	chr16:12707733-12708582	HepG2	liver:	n/a	n/a
10	POLR2A	chr16:12707233-12709090	GM12891	blood:	n/a	n/a
11	POLR2A	chr16:12706343-12709066	HepG2	liver:	n/a	n/a
12	POLR2A	chr16:12707186-12708972	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:12705362..12710268-chr16:12710311..12712475,5	K562	blood:
2	chr16:12705693..12708514-chr16:12893374..12897390,4	K562	blood:
3	chr16:12707551..12710268-chr16:12710403..12713580,3	K562	blood:

Variant related genes	Relation type
ENSG00000259899	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10500384	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10500388	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11640050	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11645561	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11646824	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11866714	0.80[MEX][hapmap]
rs16960309	0.85[EUR][1000 genomes]
rs2115105	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60172355	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62027344	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6498341	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8062155	1.00[YRI][hapmap]
rs9746526	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv571469	chr16:12670401-12715480	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv18351	chr16:12674207-12734557	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv2757629	chr16:12676745-12712199	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv2758631	chr16:12676745-12712199	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv1812058	chr16:12680270-12712059	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1051014	chr16:12683657-12722792	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1041721	chr16:12690859-12708403	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv1808513	chr16:12691653-12711233	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	esv1813801	chr16:12691653-12711233	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv905351	chr16:12697211-12721188	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv471083	chr16:12704140-12714394	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv457422	chr16:12705930-12711025	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv571478	chr16:12705930-12711025	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv1819970	chr16:12705930-12712304	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3829527	LOC92017	cis	multi-tissue	Pritchard

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12704000-12708800	Enhancers	Placenta	Placenta
2	chr16:12704800-12709400	Enhancers	Fetal Intestine Large	intestine
3	chr16:12705000-12709000	Enhancers	Fetal Intestine Small	intestine
4	chr16:12706000-12708800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr16:12706400-12709000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr16:12706400-12709000	Enhancers	Fetal Thymus	thymus
7	chr16:12706600-12708600	Enhancers	H9 Cell Line	embryonic stem cell
8	chr16:12706600-12708600	Enhancers	Thymus	Thymus
9	chr16:12706600-12708600	Enhancers	GM12878-XiMat	blood
10	chr16:12706600-12708800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr16:12706800-12708800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr16:12707200-12709000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr16:12707400-12708600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr16:12707400-12708800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr16:12707600-12709400	Enhancers	K562	blood
16	chr16:12707800-12708600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr16:12708000-12709200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr16:12708000-12713200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr16:12708200-12708600	Enhancers	A549	lung
20	chr16:12708400-12708600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr16:12708400-12713600	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links