Variant report

Variant	rs11973846
Chromosome Location	chr7:128340833-128340834
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	chr7:128332579..128336216-chr7:128338226..128341696,3	K562	blood:
2	chr7:128340595..128342111-chr7:128500707..128503271,2	K562	blood:

Variant related genes	Relation type
ENSG00000242902	Chromatin interaction
ENSG00000239722	Chromatin interaction
ENSG00000128524	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1003241	0.90[YRI][hapmap]
rs10253936	0.85[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10954193	0.90[YRI][hapmap]
rs1109552	0.90[YRI][hapmap]
rs11972335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11979987	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12668292	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12670271	0.85[YRI][hapmap]
rs12672216	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12674125	0.90[YRI][hapmap]
rs1450874	0.90[YRI][hapmap]
rs1450875	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17169024	0.90[YRI][hapmap]
rs17169357	0.90[YRI][hapmap]
rs1839595	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2290229	0.94[YRI][hapmap]
rs2402932	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs339077	0.86[CHD][hapmap]
rs3807125	0.88[TSI][hapmap]
rs4283986	0.89[MKK][hapmap];0.88[TSI][hapmap]
rs4554406	0.90[YRI][hapmap]
rs4728128	0.90[YRI][hapmap]
rs4728130	0.90[YRI][hapmap]
rs4731484	0.88[YRI][hapmap]
rs4731485	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4731503	0.90[YRI][hapmap]
rs4731507	0.86[MKK][hapmap];0.88[TSI][hapmap]
rs4731508	0.84[MKK][hapmap];0.88[TSI][hapmap]
rs55854844	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56010148	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59475830	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59955357	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61031958	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62479561	0.81[ASN][1000 genomes]
rs62481886	0.88[EUR][1000 genomes]
rs62481894	0.88[EUR][1000 genomes]
rs62481898	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62481925	0.83[EUR][1000 genomes]
rs62481947	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62483349	0.81[AMR][1000 genomes]
rs6467210	0.90[YRI][hapmap]
rs6946411	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6949056	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs6958788	0.90[YRI][hapmap]
rs6969554	0.90[YRI][hapmap]
rs73236051	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7793136	0.90[YRI][hapmap]
rs7797745	0.90[YRI][hapmap]
rs9689994	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9690750	0.87[EUR][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	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1016979	chr7:128333070-128534438	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11973846	RP11-274B21.4	cis	Nerve Tibial	GTEx
rs11973846	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx
rs11973846	OPN1SW	cis	cerebellum	SCAN
rs11973846	RP11-274B21.4	cis	Whole Blood	GTEx
rs11973846	RP11-274B21.1	cis	Adipose Subcutaneous	GTEx
rs11973846	RP11-274B21.4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128338000-128341000	Weak transcription	HMEC	breast
2	chr7:128338000-128346000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:128338600-128349000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:128339000-128358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:128339600-128342000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr7:128339800-128341000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:128339800-128343800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:128340000-128344200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:128340200-128341000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr7:128340200-128341200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
11	chr7:128340200-128344000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:128340800-128341200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
13	chr7:128340800-128341200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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