Variant report

Variant	rs6467782
Chromosome Location	chr7:138244045-138244046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:138243849..138247271-chr7:138261474..138264900,3	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10155993	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10215281	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10227693	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10232771	0.90[ASN][1000 genomes]
rs10247380	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10248731	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1030961	0.94[CEU][hapmap];0.92[ASN][1000 genomes]
rs1077772	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs1116324	0.82[ASN][1000 genomes]
rs11976614	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12112459	0.84[ASN][1000 genomes]
rs12666310	0.91[ASN][1000 genomes]
rs1363053	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1421604	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs1544733	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1616318	0.84[ASN][1000 genomes]
rs1659830	0.81[ASN][1000 genomes]
rs1673203	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1673204	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1673205	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1673206	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1673207	0.87[ASN][1000 genomes]
rs17364560	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs17461551	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1813003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1874326	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs2353354	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2353355	0.95[ASN][1000 genomes]
rs3757381	0.94[CEU][hapmap];0.90[ASN][1000 genomes]
rs3778705	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.95[ASN][1000 genomes]
rs3807155	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3807156	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3807157	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3816192	0.83[ASN][1000 genomes]
rs55723768	0.81[ASN][1000 genomes]
rs56092804	0.81[ASN][1000 genomes]
rs57407834	0.80[ASN][1000 genomes]
rs58562866	0.84[ASN][1000 genomes]
rs62485263	0.91[ASN][1000 genomes]
rs62485264	0.92[ASN][1000 genomes]
rs62487619	0.81[ASN][1000 genomes]
rs6467776	0.86[ASN][1000 genomes]
rs6467778	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs6467780	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6467783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6944764	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6948094	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6959574	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6963539	0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs6970175	0.81[ASN][1000 genomes]
rs6974877	0.81[ASN][1000 genomes]
rs728092	0.98[ASN][1000 genomes]
rs749546	0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs7795981	0.81[ASN][1000 genomes]
rs7808392	0.84[ASN][1000 genomes]
rs9791462	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9791634	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs985299	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831153	chr7:138078179-138265648	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1030956	chr7:138163169-138579519	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6467782	JHDM1D	cis	cerebellum	SCAN
rs6467782	TRIM24	cis	parietal	SCAN
rs6467782	CHRM2	cis	parietal	SCAN
rs6467782	S100A6	trans	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138213000-138244200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:138228400-138252600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:138235000-138248600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:138235000-138257400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:138235600-138245200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:138235800-138253000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:138235800-138253200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr7:138236000-138254200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:138236800-138250800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
10	chr7:138237000-138251200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
11	chr7:138237000-138251600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:138237000-138252400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr7:138237200-138252600	ZNF genes & repeats	Dnd41	blood
14	chr7:138237400-138245200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
15	chr7:138237400-138251400	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr7:138237600-138244200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
17	chr7:138238000-138245000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr7:138238000-138245600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:138238200-138244800	ZNF genes & repeats	GM12878-XiMat	blood
20	chr7:138238200-138251200	ZNF genes & repeats	Adipose Nuclei	Adipose
21	chr7:138238400-138244200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:138238400-138244400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
23	chr7:138238400-138244600	ZNF genes & repeats	Aorta	Aorta
24	chr7:138238400-138244600	ZNF genes & repeats	Pancreas	Pancrea
25	chr7:138238400-138245600	ZNF genes & repeats	Spleen	Spleen
26	chr7:138238400-138250800	ZNF genes & repeats	Thymus	Thymus
27	chr7:138238400-138251400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:138238400-138251400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
29	chr7:138238400-138251400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
30	chr7:138238400-138253600	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr7:138238600-138244200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
32	chr7:138238600-138244600	ZNF genes & repeats	Lung	lung
33	chr7:138238600-138251200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
34	chr7:138238600-138251600	ZNF genes & repeats	Brain Germinal Matrix	brain
35	chr7:138238600-138251800	ZNF genes & repeats	Fetal Muscle Leg	muscle
36	chr7:138238600-138252200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
37	chr7:138238800-138245200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:138239200-138251000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
39	chr7:138239400-138244400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:138239400-138244600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:138239400-138244600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
42	chr7:138239400-138251000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
43	chr7:138239400-138252600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
44	chr7:138239600-138244400	ZNF genes & repeats	Primary T cells from cord blood	blood
45	chr7:138239600-138245800	ZNF genes & repeats	Colonic Mucosa	Colon
46	chr7:138239600-138247000	ZNF genes & repeats	Fetal Intestine Large	intestine
47	chr7:138239600-138250800	ZNF genes & repeats	Fetal Brain Female	brain
48	chr7:138239800-138244800	ZNF genes & repeats	Fetal Lung	lung
49	chr7:138240000-138244200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr7:138240400-138245400	ZNF genes & repeats	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links