Variant report

Variant	rs6935539
Chromosome Location	chr6:167415091-167415092
allele	A/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	EBF1	chr6:167415074-167415392	GM12878	blood:	n/a	chr6:167415234-167415247 chr6:167415236-167415246 chr6:167415236-167415245 chr6:167415234-167415245

No.	Distal block	Cell Line	Cell type
1	chr6:167353995..167356024-chr6:167413983..167416895,2	K562	blood:
2	chr6:167368436..167372370-chr6:167409956..167415121,7	MCF-7	breast:
3	chr6:167369620..167371640-chr6:167412068..167415220,3	K562	blood:
4	chr6:167411701..167414538-chr6:167414813..167420401,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227598	TF binding region
MIR3939	TF binding region
ENSG00000227598	Chromatin interaction
ENSG00000213066	Chromatin interaction
ENSG00000026297	Chromatin interaction
ENSG00000272980	Chromatin interaction
ENSG00000249141	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11557915	1.00[AMR][1000 genomes]
rs16899761	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16899805	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16899816	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16899817	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2345567	1.00[AMR][1000 genomes]
rs6456145	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6899604	1.00[AMR][1000 genomes]
rs6900132	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6901171	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6907735	0.91[AFR][1000 genomes]
rs6921037	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6922071	0.80[AFR][1000 genomes]
rs6926667	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6928981	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7750975	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7754877	0.81[AFR][1000 genomes]
rs7759776	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7762128	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs911634	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
5	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1031039	chr6:167324021-167741439	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv538543	chr6:167324021-167741439	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv1026972	chr6:167335031-167671042	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167413600-167415400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr6:167413600-167415600	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr6:167413600-167419000	Weak transcription	Ovary	ovary
4	chr6:167413600-167419000	Weak transcription	Spleen	Spleen
5	chr6:167413600-167425000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:167413600-167425000	Weak transcription	Brain Substantia Nigra	brain
7	chr6:167413600-167425000	Weak transcription	Lung	lung
8	chr6:167413600-167425200	Weak transcription	Esophagus	oesophagus
9	chr6:167413600-167428600	Weak transcription	Aorta	Aorta
10	chr6:167413600-167428800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:167413600-167428800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:167413600-167438800	Weak transcription	Right Ventricle	heart
13	chr6:167413600-167449200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:167413600-167452400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:167413800-167415400	Enhancers	Fetal Brain Female	brain
16	chr6:167413800-167415600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr6:167413800-167417400	Weak transcription	Placenta	Placenta
18	chr6:167413800-167419200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:167413800-167419200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:167413800-167436800	Weak transcription	HSMMtube	muscle
21	chr6:167414000-167415200	Enhancers	Thymus	Thymus
22	chr6:167414000-167415400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:167414000-167415600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr6:167414000-167415800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:167414000-167416200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:167414200-167415200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:167414200-167415200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
28	chr6:167414200-167415200	Enhancers	Gastric	stomach
29	chr6:167414200-167415400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr6:167414200-167415400	Genic enhancers	Fetal Muscle Leg	muscle
31	chr6:167414200-167415400	Genic enhancers	Left Ventricle	heart
32	chr6:167414200-167415400	Enhancers	Pancreas	Pancrea
33	chr6:167414200-167415400	Transcr. at gene 5' and 3'	Dnd41	blood
34	chr6:167414200-167415400	Transcr. at gene 5' and 3'	HepG2	liver
35	chr6:167414200-167415400	Enhancers	HMEC	breast
36	chr6:167414200-167415400	Transcr. at gene 5' and 3'	K562	blood
37	chr6:167414200-167416200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr6:167414400-167415200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:167414400-167415200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
40	chr6:167414400-167415200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
41	chr6:167414400-167415400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr6:167414400-167415400	Genic enhancers	Fetal Thymus	thymus
43	chr6:167414400-167415600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:167414400-167415800	Enhancers	Fetal Heart	heart
45	chr6:167414400-167416000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:167414400-167416200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:167414400-167416200	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr6:167414400-167418600	Weak transcription	A549	lung
49	chr6:167414400-167419000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr6:167414400-167419400	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links