Variant report

Variant	rs56682209
Chromosome Location	chr2:48108186-48108187
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	FOS	chr2:48108082-48108242	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr2:48107946-48108294	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr2:48107852-48108295	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr2:48107880-48108300	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48102583..48106295-chr2:48106906..48109315,3	K562	blood:
2	chr2:48099053..48102786-chr2:48106081..48109104,3	K562	blood:

Variant related genes	Relation type
ENSG00000236549	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10490303	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10495948	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17036952	1.00[AMR][1000 genomes]
rs17036971	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17037021	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17037040	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17037055	0.87[EUR][1000 genomes]
rs17037062	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17037064	0.87[EUR][1000 genomes]
rs2134055	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2881863	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3136242	1.00[AMR][1000 genomes]
rs3136274	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3136286	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4381823	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56881113	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58057481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58552166	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59624704	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60118201	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60303023	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72876814	0.89[EUR][1000 genomes]
rs7560678	0.88[AFR][1000 genomes];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	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv930955	chr2:48040218-48121218	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv523013	chr2:48073117-48146122	Active TSS Weak transcription Enhancers Strong transcription 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	16 gene(s)	inside rSNPs	diseases
8	nsv874000	chr2:48078838-48291582	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48065400-48114000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:48067000-48122000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:48089800-48121000	Weak transcription	Aorta	Aorta
4	chr2:48095000-48118200	Weak transcription	NH-A	brain
5	chr2:48095200-48118400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:48095200-48127200	Weak transcription	Fetal Kidney	kidney
7	chr2:48095400-48109400	Weak transcription	Brain Germinal Matrix	brain
8	chr2:48095400-48118200	Weak transcription	HMEC	breast
9	chr2:48095400-48129600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:48096000-48109200	Weak transcription	A549	lung
11	chr2:48096000-48123400	Weak transcription	Esophagus	oesophagus
12	chr2:48097800-48123400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:48098000-48118400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:48098000-48122400	Weak transcription	Fetal Brain Male	brain
15	chr2:48098200-48109400	Weak transcription	Fetal Brain Female	brain
16	chr2:48098200-48115200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:48098200-48115400	Weak transcription	HSMM	muscle
18	chr2:48098400-48110200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:48098400-48112400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:48098400-48117400	Weak transcription	Placenta	Placenta
21	chr2:48098400-48119600	Weak transcription	Liver	Liver
22	chr2:48098400-48125000	Weak transcription	HUVEC	blood vessel
23	chr2:48098600-48109400	Weak transcription	Fetal Lung	lung
24	chr2:48098600-48117600	Weak transcription	Left Ventricle	heart
25	chr2:48098600-48119200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:48098600-48121000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:48098600-48129000	Weak transcription	Gastric	stomach
28	chr2:48098600-48129000	Weak transcription	Pancreas	Pancrea
29	chr2:48098800-48109400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:48099000-48118200	Weak transcription	NHDF-Ad	bronchial
31	chr2:48099400-48109200	Weak transcription	Hela-S3	cervix
32	chr2:48099400-48115800	Weak transcription	Fetal Heart	heart
33	chr2:48099600-48118400	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:48099800-48112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:48099800-48115200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:48100400-48115600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:48100600-48121000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:48100600-48129200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:48100800-48109200	Weak transcription	Primary B cells from cord blood	blood
40	chr2:48100800-48109800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:48100800-48109800	Weak transcription	Thymus	Thymus
42	chr2:48100800-48110400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:48100800-48110800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:48100800-48112400	Weak transcription	Right Atrium	heart
45	chr2:48100800-48120600	Weak transcription	K562	blood
46	chr2:48101000-48109200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:48101000-48109200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:48101000-48109600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:48101000-48110400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:48101000-48110600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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