Variant report

Variant	rs28634943
Chromosome Location	chr2:145088448-145088449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:145068763..145071658-chr2:145087290..145089082,2	MCF-7	breast:
2	chr2:144952090..144954781-chr2:145087114..145090082,2	K562	blood:
3	chr2:145042494..145045279-chr2:145088197..145089944,2	MCF-7	breast:
4	chr2:145075632..145077862-chr2:145087295..145090103,3	K562	blood:
5	chr2:145085974..145088514-chr2:145187860..145190773,2	K562	blood:
6	chr2:145087636..145089922-chr2:145106660..145109539,2	K562	blood:
7	chr2:145001769..145004480-chr2:145087992..145089753,2	K562	blood:

Variant related genes	Relation type
ENSG00000121964	Chromatin interaction
ENSG00000169554	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11886379	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891991	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383608	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662371	0.87[EUR][1000 genomes]
rs62169174	0.95[EUR][1000 genomes]
rs62169185	0.98[EUR][1000 genomes]
rs62169186	0.98[EUR][1000 genomes]
rs62169187	0.95[EUR][1000 genomes]
rs62169189	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169191	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169192	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169194	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722360	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6758720	0.81[AFR][1000 genomes]
rs7588281	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997840	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532755	chr2:144631279-145270874	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1006344	chr2:144657716-145334899	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv535951	chr2:144657716-145334899	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1067624	chr2:144657717-145425705	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv531413	chr2:144657717-145425705	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription 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	18 gene(s)	inside rSNPs	diseases
6	nsv532756	chr2:144746353-145315596	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1008032	chr2:144840552-145234229	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv997624	chr2:144906679-145294503	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription 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
9	nsv535952	chr2:144906679-145294503	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv532757	chr2:144922143-145263446	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv916172	chr2:144970681-145425713	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv948474	chr2:145035890-145436665	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS 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	14 gene(s)	inside rSNPs	diseases
13	nsv1004937	chr2:145079535-145159021	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145078400-145088600	Weak transcription	Ovary	ovary
2	chr2:145078400-145088600	Weak transcription	Right Ventricle	heart
3	chr2:145078400-145089200	Weak transcription	Spleen	Spleen
4	chr2:145078800-145088600	Weak transcription	HSMMtube	muscle
5	chr2:145079000-145088600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:145080800-145089000	Weak transcription	Lung	lung
7	chr2:145081000-145088600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:145082200-145088800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:145082400-145088600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:145082600-145088600	Weak transcription	Fetal Intestine Large	intestine
11	chr2:145082800-145088600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:145083000-145088600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:145083000-145089000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:145083400-145088600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:145083600-145088600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:145084600-145088600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:145084600-145088600	Weak transcription	Hela-S3	cervix
18	chr2:145084800-145089000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:145085200-145088600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:145085200-145088800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:145086200-145088600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr2:145086200-145088600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr2:145086200-145088600	Weak transcription	Psoas Muscle	Psoas
24	chr2:145086800-145088600	Weak transcription	Small Intestine	intestine
25	chr2:145087000-145088800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr2:145087200-145088800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:145087600-145088600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:145087600-145088600	Enhancers	Brain Cingulate Gyrus	brain
29	chr2:145087600-145088600	Enhancers	Brain Hippocampus Middle	brain
30	chr2:145087600-145089000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr2:145087600-145090400	Active TSS	Fetal Brain Male	brain
32	chr2:145087800-145088600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr2:145087800-145088600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:145087800-145088600	Weak transcription	A549	lung
35	chr2:145087800-145088800	Enhancers	Brain Substantia Nigra	brain
36	chr2:145087800-145089600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:145087800-145090400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:145087800-145090400	Active TSS	GM12878-XiMat	blood
39	chr2:145088000-145088600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:145088000-145088600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:145088000-145088600	Weak transcription	Brain Angular Gyrus	brain
42	chr2:145088000-145088600	Enhancers	Duodenum Mucosa	Duodenum
43	chr2:145088000-145089000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:145088000-145089000	Flanking Active TSS	Fetal Heart	heart
45	chr2:145088000-145090600	Active TSS	Fetal Kidney	kidney
46	chr2:145088200-145088600	Enhancers	NHEK	skin
47	chr2:145088200-145088800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr2:145088200-145089000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:145088200-145089400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:145088200-145089400	Flanking Active TSS	Dnd41	blood

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