Variant report

Variant	rs9840500
Chromosome Location	chr3:136621338-136621339
allele	A/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	SPI1	chr3:136621112-136621939	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136579717..136582234-chr3:136620305..136621833,2	MCF-7	breast:
2	chr3:136621285..136624241-chr3:136629189..136631419,2	K562	blood:

Variant related genes	Relation type
ENSG00000214283	TF binding region
ENSG00000158092	Chromatin interaction
ENSG00000239213	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1052620	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062352	1.00[ASN][1000 genomes]
rs13080786	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099657	0.87[AFR][1000 genomes]
rs13100192	1.00[ASN][1000 genomes]
rs13314357	1.00[ASN][1000 genomes]
rs13433683	1.00[ASN][1000 genomes]
rs13433688	1.00[ASN][1000 genomes]
rs17365792	1.00[ASN][1000 genomes]
rs1872239	1.00[ASN][1000 genomes]
rs2176269	1.00[ASN][1000 genomes]
rs28370972	1.00[ASN][1000 genomes]
rs28390205	1.00[ASN][1000 genomes]
rs28472992	1.00[ASN][1000 genomes]
rs28489326	1.00[ASN][1000 genomes]
rs28877020	1.00[ASN][1000 genomes]
rs34564818	1.00[ASN][1000 genomes]
rs34645606	1.00[ASN][1000 genomes]
rs35096613	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35100027	1.00[ASN][1000 genomes]
rs35198484	1.00[ASN][1000 genomes]
rs35210994	1.00[ASN][1000 genomes]
rs35422852	1.00[ASN][1000 genomes]
rs35428413	1.00[ASN][1000 genomes]
rs35880395	1.00[ASN][1000 genomes]
rs36109616	1.00[ASN][1000 genomes]
rs4470449	1.00[ASN][1000 genomes]
rs66509730	1.00[ASN][1000 genomes]
rs67382287	1.00[ASN][1000 genomes]
rs6767889	1.00[ASN][1000 genomes]
rs71336080	1.00[ASN][1000 genomes]
rs73230043	1.00[ASN][1000 genomes]
rs73230099	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73231903	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809269	1.00[ASN][1000 genomes]
rs9809988	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813376	1.00[ASN][1000 genomes]
rs9819856	1.00[ASN][1000 genomes]
rs9828976	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838884	1.00[ASN][1000 genomes]
rs9845862	1.00[ASN][1000 genomes]
rs9850364	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857833	1.00[ASN][1000 genomes]
rs9858560	1.00[ASN][1000 genomes]
rs9860879	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865995	1.00[ASN][1000 genomes]
rs9867325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871184	1.00[ASN][1000 genomes]
rs9873536	1.00[ASN][1000 genomes]
rs9875770	1.00[ASN][1000 genomes]
rs9877089	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9879531	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881831	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	nsv877531	chr3:136517016-136662954	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv877532	chr3:136526939-136662603	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv877533	chr3:136539689-136662954	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136592000-136622400	Weak transcription	Aorta	Aorta
2	chr3:136609400-136625200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:136613000-136622400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:136613200-136648800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:136613400-136621600	Weak transcription	Thymus	Thymus
6	chr3:136613400-136625400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:136613400-136626200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:136613600-136621400	Weak transcription	NHDF-Ad	bronchial
9	chr3:136613600-136625200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:136613600-136625200	Weak transcription	Ovary	ovary
11	chr3:136613600-136625200	Weak transcription	Pancreas	Pancrea
12	chr3:136613600-136626200	Weak transcription	HMEC	breast
13	chr3:136613600-136633600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:136613600-136638600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:136614000-136625200	Weak transcription	Gastric	stomach
16	chr3:136614000-136625200	Weak transcription	Spleen	Spleen
17	chr3:136614600-136622200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:136615600-136621400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:136616200-136621600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr3:136617200-136621800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:136617600-136621600	Enhancers	K562	blood
22	chr3:136617600-136623000	ZNF genes & repeats	GM12878-XiMat	blood
23	chr3:136617800-136622000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr3:136618200-136621600	Weak transcription	Dnd41	blood
25	chr3:136618200-136625200	Weak transcription	Left Ventricle	heart
26	chr3:136618200-136625200	Weak transcription	Right Atrium	heart
27	chr3:136618600-136624800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:136618600-136627200	Weak transcription	Small Intestine	intestine
29	chr3:136618800-136622600	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:136618800-136624200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:136619000-136621400	Weak transcription	Primary T cells from cord blood	blood
32	chr3:136619000-136621600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:136619000-136623000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:136619200-136622000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:136619200-136622200	Enhancers	Primary hematopoietic stem cells	blood
36	chr3:136619200-136622200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr3:136619200-136622200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:136619200-136625200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:136619200-136656800	Weak transcription	NHLF	lung
40	chr3:136619400-136621800	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr3:136619400-136624600	Weak transcription	Psoas Muscle	Psoas
42	chr3:136619800-136621800	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr3:136619800-136621800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr3:136619800-136622400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:136620000-136622000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:136620200-136621400	Weak transcription	Liver	Liver
47	chr3:136620200-136622600	Enhancers	Primary B cells from peripheral blood	blood
48	chr3:136620200-136623000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:136620800-136621400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:136620800-136621600	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links