Variant report

Variant	rs6948094
Chromosome Location	chr7:138257893-138257894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:138246609..138249506-chr7:138257780..138259380,2	K562	blood:
2	chr6:27100807..27103130-chr7:138256613..138259241,2	MCF-7	breast:
3	chr7:138257087..138259853-chr7:138260870..138262972,2	K562	blood:

Variant related genes	Relation type
ENSG00000196787	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10155993	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10215281	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10227693	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10232771	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10247380	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10248731	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1030961	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1077772	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.81[ASN][1000 genomes]
rs1116324	0.82[ASN][1000 genomes]
rs11976614	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[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[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1421604	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1544733	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.80[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];0.91[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1673204	0.87[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs1673205	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1673206	0.83[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1673207	0.87[ASN][1000 genomes]
rs17364560	0.91[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs17461551	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1813003	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1874326	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs2353354	0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2353355	0.95[ASN][1000 genomes]
rs3757381	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3778705	0.86[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3807155	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3807156	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3807157	0.91[CHB][hapmap];0.85[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	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6467778	0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6467780	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6467782	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]
rs6467783	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6944764	0.82[ASN][1000 genomes]
rs6946420	0.82[LWK][hapmap]
rs6954285	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6959574	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6963539	0.86[CHB][hapmap];0.85[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	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs7795981	0.81[ASN][1000 genomes]
rs7808392	0.84[ASN][1000 genomes]
rs9791462	0.90[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs9791634	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs985299	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];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
rs6948094	TRIM24	cis	parietal	SCAN
rs6948094	JHDM1D	cis	cerebellum	SCAN
rs6948094	S100A6	trans	parietal	SCAN
rs6948094	CHRM2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138242600-138272400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
2	chr7:138250200-138273800	Weak transcription	Gastric	stomach
3	chr7:138250400-138267600	Weak transcription	NHLF	lung
4	chr7:138250400-138272000	Weak transcription	Small Intestine	intestine
5	chr7:138250400-138273000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:138250600-138263800	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:138250600-138264000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:138250600-138270600	Weak transcription	Fetal Brain Male	brain
9	chr7:138250600-138271800	Weak transcription	Right Ventricle	heart
10	chr7:138250600-138273000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:138250600-138273400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:138250800-138258000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr7:138250800-138263800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:138250800-138264000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:138250800-138272400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:138250800-138272600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr7:138250800-138273200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:138251000-138264000	Weak transcription	Psoas Muscle	Psoas
19	chr7:138251000-138267800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:138251000-138272800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:138251000-138272800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr7:138251200-138272800	Strong transcription	Fetal Thymus	thymus
23	chr7:138251200-138273000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:138251400-138259000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr7:138251400-138259200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:138251400-138259600	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr7:138251400-138259600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr7:138251400-138260600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr7:138251400-138262000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr7:138251400-138263600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr7:138251400-138266200	Strong transcription	Primary B cells from cord blood	blood
32	chr7:138251400-138270800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr7:138251400-138273000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr7:138251400-138273000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:138251600-138258800	Strong transcription	Placenta	Placenta
36	chr7:138251600-138265400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr7:138251600-138273200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:138251800-138258600	Weak transcription	Fetal Heart	heart
39	chr7:138251800-138259000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr7:138251800-138264000	Weak transcription	NHDF-Ad	bronchial
41	chr7:138252000-138259000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:138252000-138264000	Weak transcription	Colonic Mucosa	Colon
43	chr7:138252000-138266600	Strong transcription	Primary T cells from cord blood	blood
44	chr7:138252000-138270800	Strong transcription	HepG2	liver
45	chr7:138252000-138272800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr7:138252200-138259000	Strong transcription	Adipose Nuclei	Adipose
47	chr7:138252200-138261200	Strong transcription	Primary B cells from peripheral blood	blood
48	chr7:138252200-138263600	Weak transcription	Colon Smooth Muscle	Colon
49	chr7:138252200-138270400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr7:138252200-138271800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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