Variant report

Variant	rs9864589
Chromosome Location	chr3:158430706-158430707
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	BHLHE40	chr3:158430554-158431343	K562	blood:	n/a	n/a
2	GATA1	chr3:158430593-158431762	PBDE	blood:	n/a	chr3:158431260-158431269 chr3:158431230-158431240

No.	Distal block	Cell Line	Cell type
1	chr3:158430342..158432825-chr3:158434955..158438595,5	K562	blood:
2	chr3:158423211..158426282-chr3:158428433..158432187,3	K562	blood:
3	chr3:158429563..158432825-chr3:158433996..158437681,6	K562	blood:
4	chr3:158429468..158431337-chr3:158439788..158442505,2	MCF-7	breast:

Variant related genes	Relation type
RARRES1	TF binding region
ENSG00000118849	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10513527	0.87[GIH][hapmap]
rs16829079	0.81[GIH][hapmap]
rs16829118	0.87[GIH][hapmap]
rs16847130	0.84[GIH][hapmap]
rs16847135	0.87[GIH][hapmap]
rs17630223	0.86[GIH][hapmap]
rs17630394	0.84[GIH][hapmap]
rs2082838	0.87[GIH][hapmap]
rs2291594	0.87[GIH][hapmap]
rs3806642	0.87[GIH][hapmap]
rs4264773	1.00[CHB][hapmap]
rs58152433	0.98[EUR][1000 genomes]
rs59192661	0.98[EUR][1000 genomes]
rs59217052	0.80[EUR][1000 genomes]
rs59918529	0.80[EUR][1000 genomes]
rs59957986	0.98[EUR][1000 genomes]
rs61387735	0.99[EUR][1000 genomes]
rs61558956	0.80[EUR][1000 genomes]
rs61696028	0.99[EUR][1000 genomes]
rs6788069	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs73015629	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73015644	0.99[EUR][1000 genomes]
rs73015651	0.81[EUR][1000 genomes]
rs73015652	0.80[EUR][1000 genomes]
rs73015654	0.80[EUR][1000 genomes]
rs73015655	0.80[EUR][1000 genomes]
rs73015657	0.80[EUR][1000 genomes]
rs73015665	1.00[EUR][1000 genomes]
rs73015669	0.98[EUR][1000 genomes]
rs73017536	0.97[EUR][1000 genomes]
rs73017539	0.95[EUR][1000 genomes]
rs73017540	0.97[EUR][1000 genomes]
rs73017541	0.97[EUR][1000 genomes]
rs7624161	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7635704	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7636023	0.87[EUR][1000 genomes]
rs7638518	0.81[GIH][hapmap]
rs7646881	0.80[CEU][hapmap];1.00[GIH][hapmap];0.80[EUR][1000 genomes]
rs7646987	0.80[CEU][hapmap];1.00[GIH][hapmap];0.80[EUR][1000 genomes]
rs9849688	0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS 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 target site	22 gene(s)	inside rSNPs	diseases
7	nsv1007141	chr3:158415840-158433128	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
8	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	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
rs9864589	RARRES1	cis	cerebellum	SCAN
rs9864589	RARRES1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158390800-158430800	Weak transcription	Right Ventricle	heart
2	chr3:158390800-158430800	Weak transcription	Stomach Mucosa	stomach
3	chr3:158390800-158432800	Weak transcription	Spleen	Spleen
4	chr3:158390800-158444200	Weak transcription	Gastric	stomach
5	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:158391000-158438800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:158397000-158443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:158397000-158448000	Weak transcription	Thymus	Thymus
9	chr3:158399600-158445400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:158403600-158438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:158408400-158443000	Weak transcription	HepG2	liver
12	chr3:158409800-158439000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:158411600-158439400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:158412200-158440800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:158412400-158439200	Weak transcription	Fetal Kidney	kidney
16	chr3:158415000-158440800	Weak transcription	Colonic Mucosa	Colon
17	chr3:158416000-158430800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:158417600-158440600	Weak transcription	Aorta	Aorta
19	chr3:158421600-158431200	Strong transcription	Primary T cells from cord blood	blood
20	chr3:158421800-158435600	Strong transcription	Fetal Intestine Small	intestine
21	chr3:158423200-158431800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:158423800-158438800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:158424200-158446000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:158425000-158431000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr3:158425200-158431000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:158425200-158431400	Strong transcription	Dnd41	blood
27	chr3:158426400-158430800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:158426400-158432400	Strong transcription	Fetal Intestine Large	intestine
29	chr3:158426400-158435200	Weak transcription	Fetal Brain Male	brain
30	chr3:158426600-158431400	Enhancers	NHDF-Ad	bronchial
31	chr3:158426600-158432400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:158426600-158436600	Strong transcription	Fetal Stomach	stomach
33	chr3:158426800-158430800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:158426800-158431200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:158426800-158432000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:158426800-158432200	Enhancers	NHLF	lung
37	chr3:158427000-158431400	Genic enhancers	A549	lung
38	chr3:158427200-158430800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:158427200-158431000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:158427200-158431400	Genic enhancers	K562	blood
41	chr3:158427200-158431400	Enhancers	Osteobl	bone
42	chr3:158427200-158432000	Strong transcription	Fetal Muscle Leg	muscle
43	chr3:158427200-158435600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:158427600-158431800	Weak transcription	Lung	lung
45	chr3:158427600-158439000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:158427600-158440600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:158427800-158430800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:158427800-158430800	Weak transcription	Left Ventricle	heart
49	chr3:158427800-158431000	Weak transcription	Hela-S3	cervix
50	chr3:158427800-158440400	Weak transcription	Primary monocytes fromperipheralblood	blood

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