Variant report

Variant	rs72939434
Chromosome Location	chr6:106959143-106959144
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	POLR2A	chr6:106957807-106960924	MCF10A-Er-Src	breast:	n/a	n/a
2	MXI1	chr6:106957694-106959152	SK-N-SH	brain:	n/a	n/a
3	E2F4	chr6:106957768-106959295	MCF10A-Er-Src	breast:	n/a	chr6:106958287-106958299
4	POLR2A	chr6:106958092-106959982	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr6:106959067-106959883	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:106955204..106959628-chr6:106966256..106969365,4	K562	blood:
2	chr6:106957571..106959305-chr6:106960058..106962439,2	MCF-7	breast:
3	chr6:106956358..106959318-chr6:106991274..106994095,2	MCF-7	breast:

Variant related genes	Relation type
AIM1	TF binding region
ENSG00000112297	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17495053	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17495248	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17495512	0.92[AMR][1000 genomes]
rs17495623	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17495678	0.92[AMR][1000 genomes]
rs17495742	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs61741114	0.86[AFR][1000 genomes]
rs66465674	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72939427	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72939431	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72939433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72939435	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72939440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72939443	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72941307	0.86[AFR][1000 genomes]
rs72941326	0.86[AFR][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	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1025510	chr6:106791080-106982400	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv538404	chr6:106791080-106982400	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106956800-106959600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr6:106957000-106959200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:106957000-106962800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:106957200-106960000	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr6:106957200-106961200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:106957200-106961600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:106957200-106962800	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr6:106957400-106959200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:106957400-106959400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
10	chr6:106957400-106959800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
11	chr6:106957400-106960200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr6:106957400-106962200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:106957400-106963400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr6:106957600-106959600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr6:106957600-106959800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr6:106957600-106961000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr6:106957800-106959400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr6:106957800-106959600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:106957800-106959800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr6:106957800-106961400	Active TSS	Right Atrium	heart
21	chr6:106958000-106959200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:106958000-106959200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:106958000-106959400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:106958000-106959400	Active TSS	Small Intestine	intestine
25	chr6:106958000-106959400	Active TSS	HSMM	muscle
26	chr6:106958000-106960000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr6:106958000-106961000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
28	chr6:106958200-106959200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:106958200-106959200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:106958200-106959600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:106958200-106959800	Bivalent Enhancer	Fetal Heart	heart
32	chr6:106958200-106961200	Active TSS	NHDF-Ad	bronchial
33	chr6:106958400-106960000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:106958400-106960000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr6:106958400-106962000	Active TSS	GM12878-XiMat	blood
36	chr6:106958400-106962200	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr6:106958600-106959200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:106958600-106959400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:106958600-106959400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
40	chr6:106958600-106959600	Weak transcription	Lung	lung
41	chr6:106958600-106961000	Active TSS	Aorta	Aorta
42	chr6:106958600-106961000	Active TSS	Gastric	stomach
43	chr6:106958600-106961400	Bivalent/Poised TSS	Psoas Muscle	Psoas
44	chr6:106958800-106959200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:106958800-106959200	Bivalent Enhancer	Brain Angular Gyrus	brain
46	chr6:106958800-106959200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
47	chr6:106958800-106959200	Bivalent Enhancer	Brain Substantia Nigra	brain
48	chr6:106958800-106959200	Bivalent Enhancer	Colon Smooth Muscle	Colon
49	chr6:106958800-106959200	Enhancers	Esophagus	oesophagus
50	chr6:106958800-106959200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle

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