Variant report

Variant	rs2967540
Chromosome Location	chr19:36964376-36964377
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36962037..36966050-chr19:36978792..36981702,4	MCF-7	breast:
2	chr19:36963358..36964984-chr19:36977934..36980406,2	K562	blood:
3	chr19:36963358..36966840-chr19:36977934..36981487,4	K562	blood:
4	chr19:36963141..36965549-chr19:36969405..36971789,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267309	Chromatin interaction
ENSG00000186017	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11665865	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11670917	0.82[AMR][1000 genomes]
rs11672024	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11673325	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12971760	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12985198	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17206393	1.00[CEU][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2385797	0.86[ASW][hapmap];0.95[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2912415	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2912423	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2912435	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2912437	0.81[GIH][hapmap]
rs2912439	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2912441	0.93[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2945946	0.81[GIH][hapmap];0.84[TSI][hapmap]
rs2945953	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2945976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967443	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2967444	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2967445	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967446	0.88[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2967449	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs2967453	0.87[AMR][1000 genomes]
rs2967505	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs2967528	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2967530	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2967531	0.95[MEX][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2967534	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2967535	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2967537	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2967539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs3096636	0.81[JPT][hapmap]
rs3107235	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3107236	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108196	0.95[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs3108203	0.81[JPT][hapmap]
rs3108209	0.81[JPT][hapmap]
rs3108543	0.81[JPT][hapmap]
rs3108545	0.81[JPT][hapmap]
rs3108546	0.81[JPT][hapmap]
rs3108549	0.86[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap]
rs3108550	0.81[JPT][hapmap]
rs3108596	0.81[JPT][hapmap]
rs3108598	0.86[CEU][hapmap];0.93[GIH][hapmap]
rs3108609	0.81[JPT][hapmap]
rs3111553	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34550124	0.82[AMR][1000 genomes]
rs34664029	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34830781	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35408779	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62113910	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62113945	0.81[AMR][1000 genomes]
rs7248477	0.81[JPT][hapmap]
rs8104181	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv1067364	chr19:36921204-36985874	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2967540	NFKBIB	cis	parietal	SCAN
rs2967540	LGALS4	cis	parietal	SCAN
rs2967540	ARHGEF1	cis	cerebellum	SCAN
rs2967540	ZNF567	Cis_1M	lymphoblastoid	RTeQTL
rs2967540	PPP1R14A	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36936400-36978400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:36941000-36979000	Weak transcription	Hela-S3	cervix
3	chr19:36942600-36966200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:36944800-36969600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:36945800-36979000	Weak transcription	Fetal Heart	heart
6	chr19:36947600-36977400	ZNF genes & repeats	Liver	Liver
7	chr19:36953200-36967600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:36953200-36967800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:36953400-36967600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:36954000-36972200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:36954400-36967800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:36955200-36966400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:36955200-36966600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:36955400-36966400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr19:36955600-36967200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:36955800-36965400	Weak transcription	NHEK	skin
17	chr19:36956000-36966000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:36956000-36966600	Strong transcription	Dnd41	blood
19	chr19:36956600-36964600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:36957200-36966600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:36957200-36966600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:36957200-36979600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:36957400-36979400	Weak transcription	NH-A	brain
24	chr19:36957600-36964400	Weak transcription	HMEC	breast
25	chr19:36957600-36965000	Strong transcription	Adipose Nuclei	Adipose
26	chr19:36958000-36965000	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr19:36958200-36964400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr19:36958200-36967600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:36958400-36965000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr19:36958800-36967000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
31	chr19:36958800-36971200	ZNF genes & repeats	A549	lung
32	chr19:36959000-36965200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:36959400-36965200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:36959600-36967200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr19:36959800-36964600	Strong transcription	Fetal Brain Female	brain
36	chr19:36960000-36966600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:36960200-36966000	Strong transcription	Fetal Muscle Leg	muscle
38	chr19:36960200-36966800	Strong transcription	Fetal Intestine Large	intestine
39	chr19:36960400-36979600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr19:36960800-36966400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
41	chr19:36960800-36966600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:36961000-36964400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr19:36961000-36964400	Strong transcription	Pancreas	Pancrea
44	chr19:36961200-36966600	Strong transcription	Left Ventricle	heart
45	chr19:36961400-36965000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:36961400-36966600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr19:36962000-36965000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr19:36962200-36964400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:36962200-36964400	Strong transcription	Brain Substantia Nigra	brain
50	chr19:36962200-36964400	Strong transcription	Thymus	Thymus

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