Variant report

Variant	rs6952900
Chromosome Location	chr7:16524455-16524456
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	chr7:16518789..16520770-chr7:16521668..16524665,2	K562	blood:
2	chr7:16523356..16525070-chr7:16684503..16686838,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136261	Chromatin interaction
ENSG00000106524	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10950624	0.85[ASN][1000 genomes]
rs10950625	0.85[ASN][1000 genomes]
rs10950626	0.86[ASN][1000 genomes]
rs11972664	0.85[ASN][1000 genomes]
rs11982808	0.85[ASN][1000 genomes]
rs12536679	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17365530	0.90[JPT][hapmap]
rs2528463	0.89[ASN][1000 genomes]
rs2528464	1.00[ASN][1000 genomes]
rs2528465	0.91[ASN][1000 genomes]
rs2704670	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2704671	0.98[ASN][1000 genomes]
rs2704672	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2704673	0.84[ASN][1000 genomes]
rs7784407	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2759514	chr7:16236162-16527390	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2758105	chr7:16272822-16527390	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1034151	chr7:16415497-16578081	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv887754	chr7:16509086-16541388	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv887755	chr7:16509086-16542364	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv887756	chr7:16520193-16566391	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6952900	ANKMY2	cis	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16519800-16526800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:16523600-16525600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:16523600-16525800	Enhancers	HMEC	breast
4	chr7:16523800-16524800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:16523800-16525600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:16524000-16525000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr7:16524000-16525400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:16524000-16525400	Enhancers	NHEK	skin
9	chr7:16524000-16525600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:16524000-16525800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:16524200-16524600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:16524200-16524600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:16524200-16524600	Enhancers	Fetal Intestine Large	intestine
14	chr7:16524200-16524600	Flanking Active TSS	NH-A	brain
15	chr7:16524200-16524800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr7:16524200-16524800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr7:16524200-16524800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr7:16524200-16524800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr7:16524200-16524800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr7:16524200-16524800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr7:16524200-16524800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr7:16524200-16524800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:16524200-16524800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:16524200-16525000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:16524200-16525000	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr7:16524200-16525000	Flanking Active TSS	A549	lung
27	chr7:16524200-16525200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr7:16524200-16525200	Enhancers	HepG2	liver
29	chr7:16524200-16525200	Enhancers	K562	blood
30	chr7:16524200-16525400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:16524400-16524800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links