Variant report

Variant	rs2541004
Chromosome Location	chr2:37228746-37228747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37192024..37194292-chr2:37227624..37230036,2	MCF-7	breast:
2	chr2:37227746..37229597-chr2:37231248..37232780,2	K562	blood:

Variant related genes	Relation type
ENSG00000115808	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10084334	0.86[ASN][1000 genomes]
rs10167385	0.88[ASN][1000 genomes]
rs10176270	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10192867	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10207971	0.84[EUR][1000 genomes]
rs10865119	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1105014	0.87[ASN][1000 genomes]
rs11124556	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11682782	0.81[ASN][1000 genomes]
rs11684340	0.84[ASN][1000 genomes]
rs11895180	0.81[ASN][1000 genomes]
rs12104444	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12105601	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13394987	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2013223	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2110992	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2110996	0.89[ASN][1000 genomes]
rs2110998	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247357	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2247935	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287107	0.85[EUR][1000 genomes]
rs2287108	0.86[EUR][1000 genomes]
rs2372913	0.89[ASN][1000 genomes]
rs2372914	0.86[ASN][1000 genomes]
rs2540998	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2541007	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2691123	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2706809	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4255943	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4606899	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4670181	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4670643	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4670647	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4670650	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58717433	0.84[EUR][1000 genomes]
rs61380056	0.81[ASN][1000 genomes]
rs62133071	0.81[ASN][1000 genomes]
rs62133078	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6544050	0.87[EUR][1000 genomes]
rs6709006	0.81[ASN][1000 genomes]
rs6712162	0.81[ASN][1000 genomes]
rs6733188	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6739171	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9309001	0.82[ASN][1000 genomes]
rs9636429	0.81[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	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv456363	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv581470	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv873879	chr2:37200033-37299145	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv581471	chr2:37213186-37257386	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37194400-37229000	Weak transcription	Gastric	stomach
2	chr2:37194800-37232400	Weak transcription	NHLF	lung
3	chr2:37195200-37252800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:37195400-37248600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:37195600-37231400	Weak transcription	Brain Angular Gyrus	brain
6	chr2:37195800-37229000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:37202000-37228800	Weak transcription	Spleen	Spleen
8	chr2:37202800-37228800	Weak transcription	Aorta	Aorta
9	chr2:37203600-37231600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:37204400-37228800	Weak transcription	Esophagus	oesophagus
11	chr2:37205200-37229400	Weak transcription	Brain Substantia Nigra	brain
12	chr2:37209000-37290200	Weak transcription	Small Intestine	intestine
13	chr2:37211400-37238200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr2:37212400-37229000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:37212800-37232000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:37214200-37248400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr2:37214600-37229000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:37214600-37229200	Weak transcription	HSMMtube	muscle
19	chr2:37215200-37231000	Weak transcription	HMEC	breast
20	chr2:37216000-37228800	Weak transcription	Right Ventricle	heart
21	chr2:37216000-37229000	Weak transcription	Brain Anterior Caudate	brain
22	chr2:37216000-37239800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:37216200-37231400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:37217000-37229000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:37219200-37256400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:37220000-37239600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:37221000-37307600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:37222200-37230800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:37222400-37232200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:37223000-37232400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:37223200-37236200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:37223400-37232000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr2:37223400-37233600	Strong transcription	Fetal Thymus	thymus
34	chr2:37223400-37236000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:37223400-37282600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:37223400-37300400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:37223600-37233800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:37223600-37235400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:37224000-37233200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr2:37224000-37233400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr2:37224000-37234600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:37224000-37236000	Strong transcription	Adipose Nuclei	Adipose
43	chr2:37224000-37236000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr2:37224000-37238600	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr2:37224000-37256000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:37224000-37270600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:37224200-37230400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr2:37224200-37232600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:37224200-37232600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:37224200-37235400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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