Variant report

Variant	rs13025994
Chromosome Location	chr2:55796220-55796221
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55793493..55797277-chr2:55842586..55846182,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12612227	0.81[AMR][1000 genomes]
rs12618859	0.83[AMR][1000 genomes]
rs12623293	0.80[AMR][1000 genomes]
rs12623937	0.91[AMR][1000 genomes]
rs12986797	0.83[AMR][1000 genomes]
rs12987272	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12993839	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12994656	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12998664	0.90[AMR][1000 genomes]
rs13001452	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13004436	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13007719	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13009649	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13015243	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13030396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1542643	0.84[AMR][1000 genomes]
rs17737233	0.90[AMR][1000 genomes]
rs1867334	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2054729	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34129478	0.81[AMR][1000 genomes]
rs34400247	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35057183	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35189503	0.80[AMR][1000 genomes]
rs35255044	0.88[AMR][1000 genomes]
rs35861320	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35968359	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs3748944	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3748952	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6753530	0.87[AMR][1000 genomes]
rs878124	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS 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 miRNA target site	30 gene(s)	inside rSNPs	diseases
7	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55769600-55816000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:55770400-55818200	Weak transcription	Small Intestine	intestine
4	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:55770800-55815800	Strong transcription	Liver	Liver
6	chr2:55775200-55798000	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr2:55779400-55798200	Strong transcription	Placenta	Placenta
8	chr2:55779400-55801400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:55779600-55797400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:55779600-55816200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:55780000-55801400	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr2:55781600-55808800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:55782200-55797400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr2:55783800-55797000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:55785000-55805000	Weak transcription	NHEK	skin
17	chr2:55787800-55797400	Weak transcription	Brain Angular Gyrus	brain
18	chr2:55788600-55816600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr2:55788800-55797000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:55788800-55808200	Weak transcription	Right Ventricle	heart
21	chr2:55788800-55825200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:55789600-55801200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:55789600-55804800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:55789800-55796400	Weak transcription	Pancreas	Pancrea
25	chr2:55789800-55799800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:55789800-55802600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:55789800-55808200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:55789800-55822800	Weak transcription	HSMMtube	muscle
29	chr2:55789800-55843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:55790200-55796400	Weak transcription	Brain Substantia Nigra	brain
31	chr2:55790200-55812800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr2:55790200-55829000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:55790200-55842400	Weak transcription	Fetal Brain Male	brain
34	chr2:55790400-55808800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:55790400-55836200	Weak transcription	Fetal Heart	heart
36	chr2:55790800-55799400	Weak transcription	Hela-S3	cervix
37	chr2:55790800-55816600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:55790800-55819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:55791200-55812200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:55791400-55805800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:55792000-55796400	Weak transcription	Fetal Brain Female	brain
42	chr2:55792000-55804000	Weak transcription	K562	blood
43	chr2:55792000-55806000	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:55792600-55798000	Strong transcription	GM12878-XiMat	blood
45	chr2:55792600-55800200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:55792600-55800600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:55792800-55797600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:55793000-55796800	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:55793200-55805200	Weak transcription	NHDF-Ad	bronchial
50	chr2:55793400-55817000	Strong transcription	Fetal Thymus	thymus

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