Variant report

Variant	rs1978878
Chromosome Location	chr15:93422482-93422483
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	GATA1	chr15:93420919-93422547	PBDE	blood:	n/a	chr15:93421878-93421895 chr15:93422371-93422382 chr15:93421942-93421952
2	CBX3	chr15:93421480-93422569	K562	blood:	n/a	n/a
3	ZNF263	chr15:93421736-93422604	HEK293-T-REx	kidney:	n/a	chr15:93421940-93421949 chr15:93422007-93422028 chr15:93421941-93421962
4	ZNF384	chr15:93421816-93422655	K562	blood:	n/a	n/a
5	TAL1	chr15:93421646-93422576	K562	blood:	n/a	chr15:93421878-93421896
6	NR2F2	chr15:93421606-93422575	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:93392783..93395116-chr15:93420649..93423095,2	K562	blood:
2	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
3	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
4	chr15:93337836..93370220-chr15:93420085..93452591,332	K562	blood:
5	chr15:93345383..93371459-chr15:93416796..93454653,318	MCF-7	breast:
6	chr15:93314139..93315981-chr15:93421509..93423581,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272888	TF binding region
CHD2	TF binding region
ENSG00000258527	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000258922	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs4778052	1.00[ASN][1000 genomes]
rs920389	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer 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	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1036560	chr15:93413594-93462163	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1978878	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93412600-93425000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:93413600-93425200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:93413800-93425200	Weak transcription	Left Ventricle	heart
4	chr15:93414000-93424200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:93418200-93423200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:93419800-93424200	Enhancers	HepG2	liver
7	chr15:93420000-93425200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr15:93420200-93422600	Enhancers	Fetal Intestine Large	intestine
9	chr15:93420200-93423200	Enhancers	Thymus	Thymus
10	chr15:93420200-93423600	Enhancers	Fetal Thymus	thymus
11	chr15:93420200-93425000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:93420200-93425000	Enhancers	Fetal Heart	heart
13	chr15:93420400-93423200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:93420400-93423200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:93420400-93424000	Weak transcription	Hela-S3	cervix
16	chr15:93420400-93425200	Weak transcription	Psoas Muscle	Psoas
17	chr15:93420600-93423600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr15:93420600-93424200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:93420600-93424600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:93420800-93422600	Enhancers	A549	lung
21	chr15:93420800-93423400	Enhancers	Primary T cells from cord blood	blood
22	chr15:93420800-93423800	Weak transcription	Fetal Stomach	stomach
23	chr15:93420800-93424200	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr15:93421000-93423200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:93421000-93424000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:93421000-93424800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr15:93421200-93422600	Enhancers	Fetal Intestine Small	intestine
28	chr15:93421400-93424200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr15:93421400-93424200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr15:93421400-93424400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr15:93421400-93424600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr15:93421400-93425200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:93421600-93422600	Flanking Active TSS	K562	blood
34	chr15:93421600-93422800	Weak transcription	Primary B cells from cord blood	blood
35	chr15:93421600-93424000	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr15:93421800-93423400	Enhancers	Dnd41	blood
37	chr15:93421800-93423600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr15:93421800-93425200	Enhancers	Placenta	Placenta
39	chr15:93421800-93426000	Weak transcription	Ovary	ovary
40	chr15:93422000-93423200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:93422000-93423200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr15:93422000-93423800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:93422000-93423800	Weak transcription	Right Atrium	heart
44	chr15:93422000-93424200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:93422000-93425000	Weak transcription	Lung	lung
46	chr15:93422000-93425200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:93422200-93422600	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr15:93422200-93423200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr15:93422200-93423200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:93422200-93423200	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links