Variant report

Variant	rs71439056
Chromosome Location	chr2:11508232-11508233
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	NFIC	chr2:11508107-11508686	ECC-1	luminal epithelium:	n/a	chr2:11508385-11508402 chr2:11508385-11508401
2	NFIC	chr2:11507959-11508697	SK-N-SH	brain:	n/a	chr2:11508385-11508402 chr2:11508385-11508401
3	PBX3	chr2:11508080-11508603	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11483340..11487694-chr2:11505828..11510815,5	K562	blood:
2	chr2:11484922..11486828-chr2:11507256..11509884,2	K562	blood:
3	chr2:11506369..11508414-chr2:11509960..11513532,3	K562	blood:

Variant related genes	Relation type
ENSG00000230952	TF binding region
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12990641	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12997263	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13015560	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13017021	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13020022	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34760292	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34887515	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35231136	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35665018	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35750432	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71439057	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active 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 miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11505400-11514400	Enhancers	Fetal Intestine Large	intestine
2	chr2:11505600-11511600	Enhancers	Fetal Intestine Small	intestine
3	chr2:11505800-11511000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:11506000-11508400	Weak transcription	Left Ventricle	heart
5	chr2:11506000-11509000	Weak transcription	Lung	lung
6	chr2:11506000-11509400	Weak transcription	Spleen	Spleen
7	chr2:11506000-11511000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:11506000-11514600	Weak transcription	K562	blood
9	chr2:11506800-11511000	Enhancers	HepG2	liver
10	chr2:11507200-11509000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr2:11507200-11511200	Enhancers	Duodenum Mucosa	Duodenum
12	chr2:11507400-11508400	Enhancers	Small Intestine	intestine
13	chr2:11507400-11508800	Enhancers	Fetal Lung	lung
14	chr2:11507400-11516200	Enhancers	Stomach Mucosa	stomach
15	chr2:11507600-11508400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr2:11507600-11508400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:11507600-11508400	Enhancers	Colonic Mucosa	Colon
18	chr2:11507600-11508400	Flanking Active TSS	Fetal Brain Male	brain
19	chr2:11507600-11508800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:11507600-11508800	Enhancers	Brain Germinal Matrix	brain
21	chr2:11507600-11509000	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr2:11507800-11508600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:11507800-11508600	Enhancers	A549	lung
24	chr2:11507800-11508800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:11507800-11509600	Enhancers	Fetal Stomach	stomach
26	chr2:11508000-11508400	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr2:11508000-11508400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr2:11508000-11508400	Enhancers	Hela-S3	cervix
29	chr2:11508000-11508600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr2:11508000-11508800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:11508000-11508800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:11508000-11508800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr2:11508000-11508800	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr2:11508000-11508800	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr2:11508000-11508800	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr2:11508000-11508800	Active TSS	Right Atrium	heart
37	chr2:11508000-11508800	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr2:11508000-11508800	Flanking Active TSS	HUVEC	blood vessel
39	chr2:11508000-11509800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr2:11508200-11508400	Active TSS	Fetal Muscle Trunk	muscle
41	chr2:11508200-11508400	Enhancers	HSMMtube	muscle
42	chr2:11508200-11508600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:11508200-11508600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:11508200-11508600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr2:11508200-11508600	Flanking Active TSS	Liver	Liver
46	chr2:11508200-11508600	Active TSS	Brain Angular Gyrus	brain
47	chr2:11508200-11508600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:11508200-11508600	Flanking Active TSS	Ovary	ovary
49	chr2:11508200-11508600	Flanking Active TSS	Psoas Muscle	Psoas
50	chr2:11508200-11508600	Flanking Active TSS	Rectal Smooth Muscle	rectum

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