Variant report

Variant	rs4713797
Chromosome Location	chr6:34458533-34458534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:34440695..34443428-chr6:34457495..34459339,2	MCF-7	breast:
2	chr6:34450820..34454475-chr6:34457385..34459321,3	K562	blood:

Variant related genes	Relation type
ENSG00000124507	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13213617	0.92[ASN][1000 genomes]
rs2395567	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]
rs3800472	0.87[GIH][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap]
rs3857563	0.80[CHB][hapmap]
rs3904668	0.81[ASN][1000 genomes]
rs4713802	0.92[ASN][1000 genomes]
rs4713805	0.91[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap]
rs7768481	0.92[ASN][1000 genomes]
rs9380441	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv462904	chr6:34416388-34493012	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv602903	chr6:34416388-34493012	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv885786	chr6:34426884-34542662	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
9	esv1813536	chr6:34455242-34545123	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	nsv885787	chr6:34458533-34546560	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4713797	ANKS1A	cis	parietal	SCAN
rs4713797	IP6K3	cis	cerebellum	SCAN
rs4713797	C6orf222	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34441400-34494000	Weak transcription	Right Atrium	heart
2	chr6:34444600-34468200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:34451000-34458800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:34454400-34459000	Weak transcription	NHEK	skin
5	chr6:34454400-34461000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:34454400-34464800	Weak transcription	Thymus	Thymus
7	chr6:34455200-34459800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr6:34456000-34458800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:34456200-34459200	Weak transcription	Right Ventricle	heart
10	chr6:34456400-34458800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:34457400-34458600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:34458000-34459400	Enhancers	Fetal Muscle Leg	muscle
13	chr6:34458000-34459600	Enhancers	Fetal Stomach	stomach
14	chr6:34458200-34458600	Enhancers	Ovary	ovary
15	chr6:34458200-34459000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr6:34458200-34459000	Enhancers	K562	blood
17	chr6:34458200-34459200	Active TSS	Stomach Smooth Muscle	stomach
18	chr6:34458200-34459400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr6:34458200-34459400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:34458200-34459400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:34458200-34459400	Enhancers	Fetal Muscle Trunk	muscle
22	chr6:34458400-34458600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:34458400-34458600	Enhancers	HSMMtube	muscle
24	chr6:34458400-34458800	Active TSS	Rectal Smooth Muscle	rectum
25	chr6:34458400-34458800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr6:34458400-34459000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr6:34458400-34459000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:34458400-34459000	Enhancers	Fetal Thymus	thymus
29	chr6:34458400-34459000	Flanking Active TSS	HSMM	muscle
30	chr6:34458400-34459200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:34458400-34459200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:34458400-34459200	Enhancers	Primary hematopoietic stem cells	blood
33	chr6:34458400-34459200	Active TSS	Colon Smooth Muscle	Colon
34	chr6:34458400-34459400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr6:34458400-34459400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr6:34458400-34459400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:34458400-34459400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:34458400-34459400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:34458400-34459600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links