Variant report

Variant	rs6912843
Chromosome Location	chr6:28904162-28904163
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	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
2	chr6:28902768..28904401-chr6:28911497..28913979,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204713	Chromatin interaction
ENSG00000204709	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1061625	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs172326	0.84[ASN][1000 genomes]
rs1794588	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs209127	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs209140	0.84[ASN][1000 genomes]
rs209147	0.81[ASN][1000 genomes]
rs209151	0.82[ASN][1000 genomes]
rs2097424	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2269553	0.82[ASN][1000 genomes]
rs2894066	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3130843	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3131067	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3132377	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3132380	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs393309	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs413972	0.84[ASN][1000 genomes]
rs429369	0.83[ASN][1000 genomes]
rs6906953	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6926892	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7740125	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7750338	0.83[ASN][1000 genomes]
rs7769221	0.83[ASN][1000 genomes]
rs876737	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9257328	0.83[ASN][1000 genomes]
rs9257395	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9257399	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9257412	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9257416	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9257425	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs929042	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6912843	ZKSCAN3	cis	cerebellum	SCAN
rs6912843	HIST1H2AE	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28901200-28906600	Weak transcription	K562	blood
2	chr6:28902800-28904600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr6:28902800-28904600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr6:28903000-28904600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:28903000-28904600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr6:28903000-28904800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:28903000-28907200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:28903000-28907600	Weak transcription	Primary B cells from cord blood	blood
9	chr6:28903200-28907200	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr6:28903600-28904600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:28903800-28907200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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