Variant report

Variant	rs72909679
Chromosome Location	chr2:39339126-39339127
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39334072..39336397-chr2:39338762..39340308,2	K562	blood:
2	chr2:39329210..39332058-chr2:39338732..39341739,3	K562	blood:
3	chr2:39338782..39340796-chr2:39455472..39457155,2	K562	blood:
4	chr2:39334897..39336790-chr2:39337544..39340262,2	K562	blood:
5	chr2:39329759..39331704-chr2:39337537..39339440,2	MCF-7	breast:
6	chr2:39338748..39341346-chr2:39343772..39345520,2	MCF-7	breast:
7	chr2:39337813..39340304-chr2:39349870..39351781,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction
ENSG00000205111	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs55649188	0.81[ASN][1000 genomes]
rs57362484	0.90[ASN][1000 genomes]
rs57866617	0.85[ASN][1000 genomes]
rs59340802	0.90[ASN][1000 genomes]
rs60718983	0.81[ASN][1000 genomes]
rs61392383	0.85[ASN][1000 genomes]
rs61456571	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6735371	0.85[ASN][1000 genomes]
rs6755453	0.90[ASN][1000 genomes]
rs72906433	0.90[ASN][1000 genomes]
rs72906442	0.90[ASN][1000 genomes]
rs72906449	0.90[ASN][1000 genomes]
rs72906454	0.90[ASN][1000 genomes]
rs72906466	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72906469	0.90[ASN][1000 genomes]
rs72906483	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs72909647	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72909674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72909676	0.81[AFR][1000 genomes]
rs72909693	0.85[ASN][1000 genomes]
rs7559174	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7571797	0.85[ASN][1000 genomes]
rs7581411	0.85[ASN][1000 genomes]
rs7588123	0.90[ASN][1000 genomes]
rs7592176	0.90[ASN][1000 genomes]
rs7605889	0.90[ASN][1000 genomes]
rs7609455	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers 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	37 gene(s)	inside rSNPs	diseases
2	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv1008198	chr2:39271472-39364035	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 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	chr2:39293800-39339400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:39294000-39345200	Weak transcription	Fetal Kidney	kidney
3	chr2:39294600-39339400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:39296400-39339400	Weak transcription	Aorta	Aorta
5	chr2:39319600-39339600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:39319800-39343200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:39321000-39344600	Weak transcription	Gastric	stomach
8	chr2:39322400-39345200	Weak transcription	Osteobl	bone
9	chr2:39322600-39344400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:39322800-39339200	Weak transcription	Fetal Thymus	thymus
11	chr2:39322800-39345200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:39323000-39339400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:39323000-39344800	Weak transcription	Primary T cells from cord blood	blood
14	chr2:39323200-39339400	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr2:39323200-39339400	Weak transcription	Fetal Intestine Large	intestine
16	chr2:39323400-39339200	Weak transcription	Dnd41	blood
17	chr2:39325000-39339400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:39327000-39344600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:39328000-39339400	Weak transcription	Thymus	Thymus
20	chr2:39328000-39346800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:39328200-39344600	Weak transcription	Hela-S3	cervix
22	chr2:39328400-39339400	Weak transcription	Esophagus	oesophagus
23	chr2:39328600-39339400	Weak transcription	Pancreas	Pancrea
24	chr2:39330000-39346800	Weak transcription	Spleen	Spleen
25	chr2:39333200-39339600	Weak transcription	Right Ventricle	heart
26	chr2:39333400-39339600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:39334000-39339200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:39334200-39345000	Weak transcription	Brain Germinal Matrix	brain
29	chr2:39334400-39339200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr2:39334600-39342600	Weak transcription	Fetal Lung	lung
31	chr2:39334600-39344400	Weak transcription	Small Intestine	intestine
32	chr2:39334600-39344600	Weak transcription	NHLF	lung
33	chr2:39334600-39345200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:39334600-39345400	Weak transcription	NH-A	brain
35	chr2:39334600-39346000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr2:39334600-39346800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:39334800-39339200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:39334800-39339200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:39334800-39343200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:39334800-39345200	Weak transcription	HSMMtube	muscle
41	chr2:39334800-39345400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:39334800-39345600	Weak transcription	HSMM	muscle
43	chr2:39335000-39339400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:39335000-39344800	Weak transcription	Brain Hippocampus Middle	brain
45	chr2:39335200-39339200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:39335200-39339400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:39335200-39341800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:39335200-39344400	Weak transcription	Liver	Liver
49	chr2:39335200-39344600	Weak transcription	Brain Anterior Caudate	brain
50	chr2:39335200-39344800	Weak transcription	Ovary	ovary

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