Variant report

Variant	rs679521
Chromosome Location	chr6:70992188-70992189
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr6:70991937-70992284	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr6:70991531-70992311	K562	blood:	n/a	chr6:70992069-70992079
3	ZNF143	chr6:70992100-70993132	H1-hESC	embryonic stem cell:	n/a	chr6:70992758-70992768
4	RCOR1	chr6:70991716-70992258	K562	blood:	n/a	n/a
5	MAX	chr6:70991592-70992623	K562	blood:	n/a	chr6:70992069-70992079
6	CHD2	chr6:70991964-70992421	H1-hESC	embryonic stem cell:	n/a	chr6:70992071-70992081
7	SIN3A	chr6:70992059-70993208	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr6:70991668-70993493	H1-hESC	embryonic stem cell:	n/a	chr6:70992069-70992079
9	CTBP2	chr6:70991548-70993379	H1-hESC	embryonic stem cell:	n/a	n/a
10	UBTF	chr6:70991761-70992300	K562	blood:	n/a	n/a
11	E2F6	chr6:70991344-70993609	H1-hESC	embryonic stem cell:	n/a	chr6:70992756-70992765 chr6:70992199-70992210 chr6:70991625-70991634 chr6:70993017-70993027 chr6:70992222-70992233 chr6:70992511-70992518
12	E2F6	chr6:70992021-70992322	K562	blood:	n/a	chr6:70992199-70992210 chr6:70992222-70992233
13	HMGN3	chr6:70991957-70992423	K562	blood:	n/a	n/a
14	TBP	chr6:70992184-70992301	K562	blood:	n/a	n/a
15	CBX3	chr6:70992017-70992369	K562	blood:	n/a	n/a
16	MAZ	chr6:70991688-70992319	K562	blood:	n/a	chr6:70992069-70992079
17	TEAD4	chr6:70992033-70992314	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr6:70991709-70992407	K562	blood:	n/a	chr6:70992069-70992079
19	MYC	chr6:70992078-70992426	H1-hESC	embryonic stem cell:	n/a	n/a
20	CHD1	chr6:70992008-70992203	H1-hESC	embryonic stem cell:	n/a	chr6:70992071-70992081
21	MAX	chr6:70991847-70993381	H1-hESC	embryonic stem cell:	n/a	chr6:70992069-70992079
22	E2F6	chr6:70991969-70992357	A549	lung:	n/a	chr6:70992199-70992210 chr6:70992222-70992233
23	USF2	chr6:70992064-70992712	H1-hESC	embryonic stem cell:	n/a	n/a
24	E2F6	chr6:70991847-70993441	H1-hESC	embryonic stem cell:	n/a	chr6:70992756-70992765 chr6:70992199-70992210 chr6:70993017-70993027 chr6:70992222-70992233 chr6:70992511-70992518
25	TBP	chr6:70991827-70993067	H1-hESC	embryonic stem cell:	n/a	n/a
26	TCF12	chr6:70992087-70992335	H1-hESC	embryonic stem cell:	n/a	chr6:70992290-70992297
27	E2F6	chr6:70991638-70992674	K562	blood:	n/a	chr6:70992199-70992210 chr6:70992222-70992233 chr6:70992511-70992518
28	POLR2A	chr6:70992095-70992269	H1-hESC	embryonic stem cell:	n/a	n/a
29	RCOR1	chr6:70991613-70992360	K562	blood:	n/a	n/a
30	MAX	chr6:70991955-70993365	H1-hESC	embryonic stem cell:	n/a	chr6:70992069-70992079
31	MAX	chr6:70991988-70992420	HepG2	liver:	n/a	chr6:70992069-70992079
32	MAX	chr6:70992003-70992308	K562	blood:	n/a	chr6:70992069-70992079
33	GTF2F1	chr6:70992109-70992619	H1-hESC	embryonic stem cell:	n/a	n/a
34	MYC	chr6:70991640-70992245	K562	blood:	n/a	chr6:70992069-70992079
35	CCNT2	chr6:70991525-70992259	K562	blood:	n/a	n/a
36	RFX5	chr6:70992073-70992207	K562	blood:	n/a	chr6:70992097-70992105
37	POLR2A	chr6:70992069-70992291	H1-hESC	embryonic stem cell:	n/a	n/a
38	E2F6	chr6:70991916-70992548	K562	blood:	n/a	chr6:70992199-70992210 chr6:70992222-70992233 chr6:70992511-70992518

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:70991484..70995327-chr6:71011821..71017351,5	K562	blood:
2	chr6:70991053..70993906-chr6:71103584..71105214,3	K562	blood:

Variant related genes	Relation type
COL9A1	TF binding region
ENSG00000237643	Chromatin interaction
ENSG00000112280	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12210123	0.87[YRI][hapmap]
rs3806104	0.80[CHB][hapmap]
rs495823	0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs9294862	0.80[CHB][hapmap]
rs9354912	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9446219	0.80[CHB][hapmap]
rs9455025	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9455026	0.80[CHB][hapmap]
rs9455027	0.80[CHB][hapmap]
rs9455031	0.80[CHB][hapmap]
rs960816	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70990000-70992800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:70990000-70993400	Enhancers	Fetal Brain Male	brain
3	chr6:70990600-70992200	Enhancers	Fetal Heart	heart
4	chr6:70991400-70992200	Bivalent Enhancer	Fetal Intestine Large	intestine
5	chr6:70991400-70993200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
6	chr6:70991600-70992200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
7	chr6:70991600-70992200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:70991600-70992200	Flanking Active TSS	K562	blood
9	chr6:70991600-70992400	Active TSS	Brain Substantia Nigra	brain
10	chr6:70991600-70992600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:70991600-70992800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:70991600-70992800	Bivalent Enhancer	Liver	Liver
13	chr6:70991600-70992800	Active TSS	Fetal Brain Female	brain
14	chr6:70991600-70993000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr6:70991600-70993000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
16	chr6:70991600-70993000	Bivalent Enhancer	Fetal Lung	lung
17	chr6:70991600-70993200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr6:70991600-70993200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
19	chr6:70991600-70993400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr6:70991800-70992200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
21	chr6:70991800-70992200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr6:70991800-70992400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:70991800-70993000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:70991800-70993000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:70991800-70993200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
26	chr6:70991800-70993200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr6:70991800-70993200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr6:70991800-70993200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
29	chr6:70991800-70993400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr6:70992000-70992200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:70992000-70992200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:70992000-70992200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:70992000-70992200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:70992000-70992200	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr6:70992000-70992200	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr6:70992000-70992200	Bivalent Enhancer	Fetal Thymus	thymus
37	chr6:70992000-70992200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
38	chr6:70992000-70992400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:70992000-70992400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
40	chr6:70992000-70992400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
41	chr6:70992000-70992400	Flanking Active TSS	Psoas Muscle	Psoas
42	chr6:70992000-70992400	Transcr. at gene 5' and 3'	Right Atrium	heart
43	chr6:70992000-70992600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:70992000-70992600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr6:70992000-70992600	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
46	chr6:70992000-70992600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
47	chr6:70992000-70992600	Bivalent Enhancer	Esophagus	oesophagus
48	chr6:70992000-70992600	Bivalent Enhancer	Left Ventricle	heart
49	chr6:70992000-70992600	Bivalent Enhancer	Stomach Mucosa	stomach
50	chr6:70992000-70992800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell

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