Variant report

Variant	rs6678164
Chromosome Location	chr1:154516571-154516572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153963702..153965277-chr1:154515258..154516911,2	K562	blood:
2	chr1:154511865..154514048-chr1:154515510..154518337,2	K562	blood:
3	chr1:154515410..154518296-chr1:154526483..154528570,2	K562	blood:
4	chr1:154297860..154300046-chr1:154515392..154517289,2	K562	blood:
5	chr1:154515311..154517020-chr1:154530616..154532196,2	K562	blood:
6	chr1:154512548..154514839-chr1:154516013..154517620,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHRNB2-1	chr1:154516439-154516586	NONHSAT006621

No data

Variant related genes	Relation type
ENSG00000160714	Chromatin interaction
ENSG00000143515	Chromatin interaction
ENSG00000163239	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10752642	0.83[ASW][hapmap];0.85[YRI][hapmap]
rs11265605	1.00[EUR][1000 genomes]
rs11265627	0.85[YRI][hapmap]
rs11265630	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1194591	1.00[EUR][1000 genomes]
rs1817688	1.00[EUR][1000 genomes]
rs2340487	1.00[EUR][1000 genomes]
rs4072391	0.84[YRI][hapmap]
rs4078519	1.00[EUR][1000 genomes]
rs4240873	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4288587	0.84[YRI][hapmap]
rs4393148	0.88[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4474240	0.80[LWK][hapmap];0.90[MKK][hapmap];0.81[YRI][hapmap]
rs4518898	0.85[YRI][hapmap]
rs4520411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845369	1.00[EUR][1000 genomes]
rs4845632	0.94[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845646	0.94[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55649582	1.00[EUR][1000 genomes]
rs6427694	0.82[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6427716	0.83[ASW][hapmap];0.85[YRI][hapmap]
rs6670375	0.83[ASW][hapmap];0.85[YRI][hapmap]
rs6681961	0.93[AFR][1000 genomes]
rs6683078	0.94[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6684225	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6685108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6687112	0.83[ASW][hapmap];0.85[YRI][hapmap]
rs6691727	0.83[ASW][hapmap];0.85[YRI][hapmap]
rs7513603	0.83[ASW][hapmap];0.85[YRI][hapmap]
rs7515974	0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7529744	1.00[MEX][hapmap]
rs7530737	0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7537595	1.00[EUR][1000 genomes]
rs7539745	0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs7556118	1.00[EUR][1000 genomes]
rs9659545	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9728545	0.94[AFR][1000 genomes]
rs9804125	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154492800-154521400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:154497600-154521200	Weak transcription	Spleen	Spleen
3	chr1:154513600-154528400	Weak transcription	Right Atrium	heart
4	chr1:154513800-154517400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:154514200-154519400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:154515400-154521400	Weak transcription	Esophagus	oesophagus
7	chr1:154515800-154516600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr1:154516000-154516600	Bivalent Enhancer	Placenta	Placenta
9	chr1:154516000-154521400	Weak transcription	Gastric	stomach
10	chr1:154516200-154516600	Enhancers	Lung	lung
11	chr1:154516400-154516800	Enhancers	Pancreas	Pancrea
12	chr1:154516400-154516800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr1:154516400-154517000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:154516400-154517000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr1:154516400-154520000	Weak transcription	Right Ventricle	heart
16	chr1:154516400-154520800	Weak transcription	Adipose Nuclei	Adipose
17	chr1:154516400-154521200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:154516400-154521200	Weak transcription	HUVEC	blood vessel

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