Variant report

Variant	rs4774929
Chromosome Location	chr15:57611294-57611295
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	YY1	chr15:57611212-57611453	K562	blood:	n/a	chr15:57611347-57611369 chr15:57611345-57611364 chr15:57611350-57611358

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57596677..57601983-chr15:57611239..57618411,9	K562	blood:
2	chr15:57022824..57027100-chr15:57611258..57614634,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCF12-2	chr15:57611129-57611535	XLOC_011265
2	lnc-TCF12-2	chr15:57611283-57611654	NONHSAT044069

Variant related genes	Relation type
ENSG00000260172	TF binding region
ENSG00000247982	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16977399	0.84[JPT][hapmap]
rs2248205	0.92[EUR][1000 genomes]
rs2440943	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4774930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised 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	49 gene(s)	inside rSNPs	diseases
2	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57599400-57612800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr15:57599600-57612400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:57599600-57612800	Weak transcription	GM12878-XiMat	blood
4	chr15:57599600-57614200	Weak transcription	Small Intestine	intestine
5	chr15:57599600-57617800	Weak transcription	Spleen	Spleen
6	chr15:57602800-57617000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:57603200-57611400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:57604200-57612800	Weak transcription	Primary B cells from cord blood	blood
9	chr15:57605000-57619400	Weak transcription	Pancreas	Pancrea
10	chr15:57605600-57611800	Weak transcription	Fetal Stomach	stomach
11	chr15:57605600-57612400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:57605600-57612400	Weak transcription	Fetal Brain Male	brain
13	chr15:57605600-57612800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:57605600-57614400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr15:57609400-57612400	Weak transcription	Right Atrium	heart
16	chr15:57611000-57611400	Enhancers	Primary B cells from peripheral blood	blood
17	chr15:57611000-57611600	ZNF genes & repeats	K562	blood
18	chr15:57611000-57612000	ZNF genes & repeats	Fetal Intestine Large	intestine
19	chr15:57611000-57613000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:57611200-57611400	Enhancers	Stomach Mucosa	stomach
21	chr15:57611200-57611600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:57611200-57612400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:57611200-57615000	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links