Variant report

Variant	rs6739827
Chromosome Location	chr2:10113504-10113505
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10113040..10115115-chr2:10116343..10118491,3	MCF-7	breast:
2	chr2:10102444..10109047-chr2:10109192..10115495,9	MCF-7	breast:
3	chr2:10090548..10095647-chr2:10110720..10115558,5	MCF-7	breast:
4	chr2:10109306..10112948-chr2:10113189..10116781,5	MCF-7	breast:
5	chr2:10090250..10093240-chr2:10111016..10113774,2	K562	blood:
6	chr2:9984016..9986818-chr2:10112280..10114129,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134317	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11674576	0.94[ASN][1000 genomes]
rs11690988	0.94[ASN][1000 genomes]
rs11883961	0.94[ASN][1000 genomes]
rs11886114	0.94[ASN][1000 genomes]
rs11886486	0.94[ASN][1000 genomes]
rs11887890	0.94[ASN][1000 genomes]
rs11889061	0.94[ASN][1000 genomes]
rs11902236	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11902932	0.94[ASN][1000 genomes]
rs13401891	0.86[ASN][1000 genomes]
rs16867262	0.92[ASN][1000 genomes]
rs16867266	0.92[ASN][1000 genomes]
rs17455130	0.94[ASN][1000 genomes]
rs1897164	0.94[ASN][1000 genomes]
rs2003911	0.94[ASN][1000 genomes]
rs2012320	0.92[ASN][1000 genomes]
rs2116014	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116015	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163336	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791761	0.85[ASN][1000 genomes]
rs3791763	0.94[ASN][1000 genomes]
rs3791764	0.94[ASN][1000 genomes]
rs3828262	0.86[ASN][1000 genomes]
rs41264205	0.94[ASN][1000 genomes]
rs4482455	0.89[ASN][1000 genomes]
rs4635506	0.89[ASN][1000 genomes]
rs59345896	0.94[ASN][1000 genomes]
rs66920316	0.94[ASN][1000 genomes]
rs67093290	0.94[ASN][1000 genomes]
rs6711126	0.94[ASN][1000 genomes]
rs6716765	0.94[ASN][1000 genomes]
rs6721359	0.94[ASN][1000 genomes]
rs67223835	0.94[ASN][1000 genomes]
rs6725087	0.94[ASN][1000 genomes]
rs6735737	0.89[ASN][1000 genomes]
rs6749296	0.94[ASN][1000 genomes]
rs6750565	0.94[ASN][1000 genomes]
rs6750946	0.94[ASN][1000 genomes]
rs72784430	0.87[ASN][1000 genomes]
rs72784434	0.94[ASN][1000 genomes]
rs72784441	0.94[ASN][1000 genomes]
rs72784463	0.94[ASN][1000 genomes]
rs730922	0.94[ASN][1000 genomes]
rs73162262	0.94[ASN][1000 genomes]
rs73162264	0.94[ASN][1000 genomes]
rs73913937	0.94[ASN][1000 genomes]
rs73913938	0.94[ASN][1000 genomes]
rs891499	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription 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	32 gene(s)	inside rSNPs	diseases
7	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10094800-10124400	Weak transcription	Fetal Intestine Large	intestine
2	chr2:10099000-10115400	Strong transcription	Liver	Liver
3	chr2:10101000-10117000	Strong transcription	HepG2	liver
4	chr2:10101400-10144800	Weak transcription	Brain Germinal Matrix	brain
5	chr2:10101600-10116400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:10101600-10136400	Weak transcription	Brain Angular Gyrus	brain
7	chr2:10101800-10114800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:10102200-10136400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:10102400-10116600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:10104600-10130200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:10106000-10119800	Weak transcription	Dnd41	blood
12	chr2:10109400-10115600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:10110200-10117800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:10110400-10113600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr2:10110400-10115200	Bivalent Enhancer	Fetal Lung	lung
16	chr2:10110400-10116200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:10110600-10114000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:10110600-10117200	Enhancers	NHDF-Ad	bronchial
19	chr2:10110800-10113600	Enhancers	Placenta	Placenta
20	chr2:10111000-10113600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:10111000-10113600	Enhancers	NHEK	skin
22	chr2:10111000-10114800	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:10111000-10116200	Weak transcription	Adipose Nuclei	Adipose
24	chr2:10111000-10117000	Enhancers	NHLF	lung
25	chr2:10111200-10113800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:10111200-10116000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:10111200-10116400	Weak transcription	Psoas Muscle	Psoas
28	chr2:10111400-10115800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:10112000-10113600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:10112200-10113600	Enhancers	HMEC	breast
31	chr2:10112400-10113600	Enhancers	Stomach Mucosa	stomach
32	chr2:10112400-10113800	Enhancers	Fetal Kidney	kidney
33	chr2:10112600-10113600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:10112600-10113600	Genic enhancers	Esophagus	oesophagus
35	chr2:10112600-10113600	Enhancers	Gastric	stomach
36	chr2:10112600-10113600	Enhancers	Pancreas	Pancrea
37	chr2:10112600-10113800	Enhancers	Hela-S3	cervix
38	chr2:10112600-10114200	Enhancers	K562	blood
39	chr2:10112600-10116800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:10112600-10117000	Enhancers	NH-A	brain
41	chr2:10112600-10117000	Enhancers	Osteobl	bone
42	chr2:10112600-10117200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr2:10112800-10113600	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr2:10112800-10113600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr2:10112800-10113600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:10112800-10113600	Enhancers	HSMM	muscle
47	chr2:10112800-10114000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:10112800-10114000	Enhancers	A549	lung
49	chr2:10112800-10114200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:10113200-10113600	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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