Variant report

Variant	rs10924989
Chromosome Location	chr1:247500650-247500651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247500532..247503648-chr1:247521272..247523608,4	K562	blood:
2	chr1:247484997..247486937-chr1:247500462..247503140,2	K562	blood:
3	chr1:247497896..247501644-chr1:247501987..247504336,4	MCF-7	breast:
4	chr1:247498783..247501107-chr1:247612451..247615319,2	K562	blood:

Variant related genes	Relation type
ENSG00000177535	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10754542	0.89[ASN][1000 genomes]
rs10924985	0.89[ASN][1000 genomes]
rs11578583	0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1192830	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1192831	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1192832	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12035515	0.81[ASN][1000 genomes]
rs1204493	0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1616299	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1771943	0.81[ASN][1000 genomes]
rs1771948	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1778544	0.85[ASN][1000 genomes]
rs1778546	0.85[ASN][1000 genomes]
rs1778549	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2153631	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs3850824	0.86[ASN][1000 genomes]
rs4320815	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4925532	0.89[ASN][1000 genomes]
rs4925533	0.89[ASN][1000 genomes]
rs4925534	0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4925615	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4925621	0.84[ASN][1000 genomes]
rs56037169	0.86[ASN][1000 genomes]
rs56399534	0.86[ASN][1000 genomes]
rs6674425	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6692645	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7418221	0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7528202	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs7540329	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs7552292	0.85[ASN][1000 genomes]
rs875883	0.87[ASN][1000 genomes]
rs9426180	0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs9426181	0.88[ASN][1000 genomes]
rs9426182	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9426233	0.83[ASN][1000 genomes]
rs9725334	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[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	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
3	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a
5	nsv873439	chr1:247486736-247549220	Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a
6	esv1799864	chr1:247494789-247500650	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10924989	ZNF496	cis	Nerve Tibial	GTEx
rs10924989	ZNF496	cis	cerebellum	SCAN
rs10924989	ZNF496	cis	Esophagus Muscularis	GTEx
rs10924989	EFCAB2	cis	parietal	SCAN
rs10924989	ZNF496	cis	lung	GTEx
rs10924989	ZNF496	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247496200-247503000	Weak transcription	Aorta	Aorta
2	chr1:247496400-247501600	Enhancers	Primary hematopoietic stem cells	blood
3	chr1:247496400-247511000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:247496600-247501000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:247496600-247501000	Weak transcription	NHDF-Ad	bronchial
6	chr1:247496600-247505800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:247496600-247506000	Weak transcription	HSMMtube	muscle
8	chr1:247496600-247511000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:247496800-247500800	Weak transcription	Ovary	ovary
10	chr1:247496800-247501200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:247496800-247501200	Genic enhancers	Fetal Muscle Leg	muscle
12	chr1:247496800-247501400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:247496800-247502000	Weak transcription	HSMM	muscle
14	chr1:247496800-247502200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:247496800-247503000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:247496800-247507200	Weak transcription	Fetal Intestine Large	intestine
17	chr1:247496800-247510200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:247497000-247501600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:247497000-247503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:247497000-247504000	Weak transcription	Stomach Mucosa	stomach
21	chr1:247497000-247511200	Weak transcription	Esophagus	oesophagus
22	chr1:247497200-247500800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr1:247497200-247500800	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:247497200-247502200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:247497200-247503000	Weak transcription	NHEK	skin
26	chr1:247497200-247505800	Weak transcription	Brain Substantia Nigra	brain
27	chr1:247497200-247506200	Weak transcription	HMEC	breast
28	chr1:247497200-247509800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:247497200-247516000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:247497400-247503000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:247497400-247511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:247497400-247511400	Weak transcription	Primary T cells from cord blood	blood
33	chr1:247497800-247501400	Enhancers	H1 Cell Line	embryonic stem cell
34	chr1:247497800-247502800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:247497800-247506400	Weak transcription	GM12878-XiMat	blood
36	chr1:247498000-247502800	Weak transcription	Hela-S3	cervix
37	chr1:247498200-247501400	Weak transcription	HepG2	liver
38	chr1:247498200-247501800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:247498200-247501800	Weak transcription	Psoas Muscle	Psoas
40	chr1:247498400-247501200	Enhancers	K562	blood
41	chr1:247498400-247501600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:247498400-247502000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:247498400-247503000	Weak transcription	A549	lung
44	chr1:247498400-247503200	Weak transcription	Fetal Intestine Small	intestine
45	chr1:247498800-247500800	Weak transcription	Pancreas	Pancrea
46	chr1:247498800-247502600	Weak transcription	Dnd41	blood
47	chr1:247498800-247505200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:247499000-247500800	Weak transcription	Placenta	Placenta
49	chr1:247499000-247501600	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr1:247499200-247500800	Weak transcription	Fetal Brain Female	brain

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