Variant report

Variant	rs9861291
Chromosome Location	chr3:178791678-178791679
allele	C/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	BHLHE40	chr3:178791670-178791863	GM12878	blood:	n/a	n/a
2	RUNX3	chr3:178791532-178792323	GM12878	blood:	n/a	chr3:178791784-178791793 chr3:178791784-178791793
3	RUNX3	chr3:178791564-178792089	GM12878	blood:	n/a	chr3:178791784-178791793 chr3:178791784-178791793
4	YY1	chr3:178791647-178791942	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:178780519..178783087-chr3:178791350..178793561,2	MCF-7	breast:
2	chr3:178790486..178793046-chr3:179039770..179041541,2	K562	blood:

Variant related genes	Relation type
ZMAT3	TF binding region
ENSG00000121864	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10936990	0.88[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs2677760	0.89[CEU][hapmap]
rs3729679	0.85[CEU][hapmap]
rs66667727	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription 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	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9861291	FAM131A	cis	parietal	SCAN
rs9861291	ZMAT3	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178790000-178806200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:178790200-178792000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:178790200-178792200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:178790200-178792800	Enhancers	Fetal Thymus	thymus
5	chr3:178790200-178793400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:178790200-178793400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr3:178790400-178791800	Enhancers	GM12878-XiMat	blood
8	chr3:178790400-178791800	Enhancers	K562	blood
9	chr3:178790400-178792000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:178790400-178792000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:178790400-178792000	Weak transcription	Dnd41	blood
12	chr3:178790400-178792200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:178790400-178792400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:178790400-178792600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:178790400-178792600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:178790400-178792800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr3:178790400-178793200	Enhancers	Primary T cells from cord blood	blood
18	chr3:178790400-178793200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr3:178790400-178793400	Enhancers	Primary B cells from cord blood	blood
20	chr3:178790400-178797200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:178791000-178793200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:178791000-178794200	Enhancers	Primary B cells from peripheral blood	blood
23	chr3:178791200-178792200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:178791200-178792200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:178791200-178792800	Enhancers	Thymus	Thymus
26	chr3:178791400-178793400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:178791600-178792600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr3:178791600-178793200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:178791600-178793400	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links