Variant report

Variant	rs2028686
Chromosome Location	chr4:99836538-99836539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99565530..99567137-chr4:99836060..99837729,2	K562	blood:
2	chr4:99828644..99831249-chr4:99834721..99838049,3	K562	blood:
3	chr4:99832216..99838344-chr4:99849441..99852575,6	MCF-7	breast:
4	chr4:99833130..99837716-chr4:99849247..99851294,5	MCF-7	breast:
5	chr4:99834371..99837889-chr4:99846144..99848239,3	MCF-7	breast:
6	chr4:99833919..99835946-chr4:99836497..99839831,4	K562	blood:

Variant related genes	Relation type
ENSG00000263923	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000249055	Chromatin interaction
ENSG00000238449	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10516438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11726503	0.86[CHB][hapmap]
rs12507214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12649066	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12651447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028687	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3749547	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55807127	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56669998	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6532769	0.85[JPT][hapmap]
rs66467917	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66761677	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66809909	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67517620	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72692608	0.84[EUR][1000 genomes]
rs72692611	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7654109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs961757	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879654	chr4:99748988-99877402	Weak transcription Enhancers Strong transcription Active TSS Flanking 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	31 gene(s)	inside rSNPs	diseases
3	nsv879655	chr4:99783733-99843113	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99802800-99849000	Weak transcription	Aorta	Aorta
2	chr4:99804400-99848800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:99804600-99838400	Weak transcription	Esophagus	oesophagus
4	chr4:99807200-99849000	Weak transcription	Colonic Mucosa	Colon
5	chr4:99808000-99841400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:99808600-99849000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:99815800-99848200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr4:99816600-99847200	Weak transcription	Fetal Brain Male	brain
9	chr4:99823000-99841600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:99823000-99842600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:99823000-99845600	Weak transcription	Hela-S3	cervix
12	chr4:99823000-99847200	Weak transcription	Thymus	Thymus
13	chr4:99823000-99848800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:99823000-99849000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:99823000-99849200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:99823200-99839600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:99823200-99847800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:99823200-99848000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:99823200-99848600	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:99823200-99848800	Weak transcription	Placenta	Placenta
21	chr4:99824200-99846800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:99825200-99841400	Weak transcription	Psoas Muscle	Psoas
23	chr4:99825800-99837200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:99827000-99841000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:99827000-99848200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:99827200-99846000	Weak transcription	Fetal Intestine Large	intestine
27	chr4:99827400-99837800	Weak transcription	HepG2	liver
28	chr4:99827600-99838600	Weak transcription	HSMM	muscle
29	chr4:99827600-99846400	Weak transcription	NH-A	brain
30	chr4:99827600-99846600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:99828000-99841200	Weak transcription	Osteobl	bone
32	chr4:99829000-99837400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr4:99829000-99837800	Weak transcription	Fetal Heart	heart
34	chr4:99829000-99838800	Weak transcription	Right Ventricle	heart
35	chr4:99829600-99846800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr4:99830000-99837000	Weak transcription	Primary B cells from cord blood	blood
37	chr4:99830000-99848200	Weak transcription	Fetal Kidney	kidney
38	chr4:99830200-99846600	Weak transcription	A549	lung
39	chr4:99830400-99838000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr4:99830400-99841400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:99831000-99837800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr4:99831000-99837800	Weak transcription	Brain Substantia Nigra	brain
43	chr4:99831000-99838000	Weak transcription	Ovary	ovary
44	chr4:99831000-99838800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:99831000-99838800	Weak transcription	Fetal Intestine Small	intestine
46	chr4:99831000-99849200	Weak transcription	Gastric	stomach
47	chr4:99831200-99837400	Weak transcription	K562	blood
48	chr4:99831200-99838000	Weak transcription	Dnd41	blood
49	chr4:99831200-99839800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:99831200-99841200	Weak transcription	HMEC	breast

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