Variant report

Variant	rs2131109
Chromosome Location	chr3:49704987-49704988
allele	A/G
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: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1050088	0.85[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs1060962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130199	0.86[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap]
rs11130212	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11130213	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1131095	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs11709525	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs11718165	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11919311	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12490267	0.87[EUR][1000 genomes]
rs12497288	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1352890	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1568661	0.86[CHD][hapmap];0.94[GIH][hapmap]
rs1801143	0.85[GIH][hapmap]
rs1826347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs1873625	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs1873626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2005557	1.00[CEU][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2131104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2329020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2960548	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3197999	0.92[CHD][hapmap];0.83[GIH][hapmap]
rs34762726	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs35007338	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35404120	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35701831	0.94[GIH][hapmap];0.83[MEX][hapmap]
rs3811697	0.85[GIH][hapmap]
rs3870338	0.86[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs3924462	0.86[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap]
rs4283605	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs4625	0.85[GIH][hapmap]
rs4855835	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4855839	0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap]
rs4855847	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4855852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4855859	0.86[CHD][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap]
rs4855864	0.86[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs4855881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4855883	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4855884	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6765869	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6766131	0.85[GIH][hapmap]
rs6767878	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6782577	0.96[CEU][hapmap]
rs6803222	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs7622302	0.85[GIH][hapmap]
rs7637999	0.86[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap]
rs9812791	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs9822268	0.92[CHD][hapmap];0.88[GIH][hapmap]
rs9823546	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9827708	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs9836291	0.86[ASN][1000 genomes]
rs9837027	0.85[GIH][hapmap]
rs9853683	0.85[GIH][hapmap]
rs9858213	1.00[JPT][hapmap]
rs9858280	0.85[GIH][hapmap]
rs9858542	0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9875617	0.85[GIH][hapmap]
rs9882740	0.92[CHD][hapmap];0.88[GIH][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2131109	CCDC71	cis	cerebellum	SCAN
rs2131109	CELSR3	cis	cerebellum	SCAN
rs2131109	ALS2CL	cis	cerebellum	SCAN
rs2131109	WDR6	cis	lymphoblastoid	seeQTL
rs2131109	CISH	cis	lymphoblastoid	seeQTL
rs2131109	ARIH2	cis	parietal	SCAN
rs2131109	IP6K2	cis	cerebellum	SCAN

Chromatin state (count:51 , 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	chr3:49703400-49705200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:49703400-49709400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:49703600-49705200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:49703600-49705200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:49703600-49705800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:49703600-49706200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:49703600-49709000	Weak transcription	Placenta	Placenta
21	chr3:49703600-49710600	Weak transcription	Left Ventricle	heart
22	chr3:49703600-49710600	Weak transcription	Right Ventricle	heart
23	chr3:49703600-49710600	Weak transcription	Spleen	Spleen
24	chr3:49703800-49705400	Weak transcription	HMEC	breast
25	chr3:49703800-49705600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:49703800-49706000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:49703800-49710600	Enhancers	Liver	Liver
28	chr3:49703800-49710600	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:49704000-49705200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:49704000-49706800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:49704000-49707000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:49704200-49710600	Weak transcription	Gastric	stomach
33	chr3:49704400-49705000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr3:49704400-49705000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:49704400-49705000	Genic enhancers	Brain Anterior Caudate	brain
36	chr3:49704400-49705400	Genic enhancers	Brain Inferior Temporal Lobe	brain
37	chr3:49704400-49706000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:49704400-49706200	Enhancers	HSMMtube	muscle
39	chr3:49704400-49710600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:49704600-49705000	Enhancers	HepG2	liver
41	chr3:49704600-49705600	Weak transcription	HSMM	muscle
42	chr3:49704600-49705600	Weak transcription	NH-A	brain
43	chr3:49704600-49706200	Enhancers	Brain Angular Gyrus	brain
44	chr3:49704600-49709000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:49704600-49709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:49704600-49710600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:49704600-49710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:49704800-49705200	Weak transcription	Fetal Intestine Large	intestine
49	chr3:49704800-49705200	Weak transcription	Fetal Intestine Small	intestine
50	chr3:49704800-49705400	Strong transcription	Brain Cingulate Gyrus	brain

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