Variant report

Variant	rs9823546
Chromosome Location	chr3:49705512-49705513
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49698247..49700593-chr3:49704782..49707775,2	MCF-7	breast:
2	chr3:49588369..49592998-chr3:49704328..49708705,5	K562	blood:
3	chr3:49704547..49706836-chr3:49714459..49716398,2	MCF-7	breast:
4	chr3:49588369..49590572-chr3:49704819..49707525,2	K562	blood:
5	chr3:49704645..49708091-chr3:49709856..49713074,5	MCF-7	breast:
6	chr3:49572703..49574370-chr3:49703529..49706014,2	K562	blood:
7	chr3:49598290..49599982-chr3:49704902..49707508,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226913	Chromatin interaction
ENSG00000164061	Chromatin interaction
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1060962	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11130212	0.86[ASN][1000 genomes]
rs11130213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1131095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11709525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11710037	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11718165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720597	0.82[AMR][1000 genomes]
rs11917431	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11921590	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13064576	0.82[AMR][1000 genomes]
rs13085791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13316695	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1352890	0.81[ASN][1000 genomes]
rs1801143	1.00[CEU][hapmap]
rs1873625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1873626	0.81[ASN][1000 genomes]
rs2005557	0.91[ASN][1000 genomes]
rs2131104	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2131109	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2172252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2329020	0.81[ASN][1000 genomes]
rs3197999	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34762726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35007338	0.81[ASN][1000 genomes]
rs35404120	0.81[ASN][1000 genomes]
rs3811697	1.00[CEU][hapmap]
rs4283605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4625	1.00[CEU][hapmap]
rs4855847	0.81[ASN][1000 genomes]
rs4855883	0.85[ASN][1000 genomes]
rs4855884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6765869	0.91[ASN][1000 genomes]
rs6766131	1.00[CEU][hapmap]
rs6770670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6803222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7614725	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7622302	1.00[CEU][hapmap]
rs7633271	1.00[CEU][hapmap]
rs9811982	1.00[CEU][hapmap]
rs9812791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9822268	1.00[CEU][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9824092	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9827021	1.00[CEU][hapmap]
rs9827708	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9833611	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9836291	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837027	1.00[CEU][hapmap]
rs9837341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9837520	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9853683	1.00[CEU][hapmap]
rs9858213	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9858280	1.00[CEU][hapmap]
rs9858542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862080	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9875617	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs9882740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9823546	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9823546	FAM212A	cis	Muscle Skeletal	GTEx
rs9823546	IHPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
2	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
3	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
4	chr3:49687600-49705800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:49690400-49710600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:49692200-49710400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49695200-49710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49700000-49710600	Weak transcription	Fetal Brain Male	brain
9	chr3:49701800-49707000	Enhancers	Fetal Muscle Leg	muscle
10	chr3:49702000-49707400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:49702400-49705600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:49702400-49710600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:49702800-49707400	Enhancers	Pancreas	Pancrea
14	chr3:49703400-49709400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:49703600-49705800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:49703600-49706200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:49703600-49709000	Weak transcription	Placenta	Placenta
18	chr3:49703600-49710600	Weak transcription	Left Ventricle	heart
19	chr3:49703600-49710600	Weak transcription	Right Ventricle	heart
20	chr3:49703600-49710600	Weak transcription	Spleen	Spleen
21	chr3:49703800-49705600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:49703800-49706000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:49703800-49710600	Enhancers	Liver	Liver
24	chr3:49703800-49710600	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:49704000-49706800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:49704000-49707000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:49704200-49710600	Weak transcription	Gastric	stomach
28	chr3:49704400-49706000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:49704400-49706200	Enhancers	HSMMtube	muscle
30	chr3:49704400-49710600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:49704600-49705600	Weak transcription	HSMM	muscle
32	chr3:49704600-49705600	Weak transcription	NH-A	brain
33	chr3:49704600-49706200	Enhancers	Brain Angular Gyrus	brain
34	chr3:49704600-49709000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:49704600-49709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:49704600-49710600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:49704600-49710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:49704800-49710600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:49705000-49705800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:49705000-49705800	Weak transcription	Hela-S3	cervix
41	chr3:49705000-49707000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr3:49705000-49710600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr3:49705200-49705600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:49705200-49705600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:49705200-49705600	Enhancers	Brain Anterior Caudate	brain
46	chr3:49705200-49705600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:49705200-49706000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr3:49705200-49706200	Enhancers	Fetal Intestine Large	intestine
49	chr3:49705200-49706200	Enhancers	Fetal Intestine Small	intestine
50	chr3:49705200-49707200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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