Variant report

Variant	rs2030816
Chromosome Location	chr3:119228607-119228608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119186319..119187917-chr3:119227987..119230729,2	MCF-7	breast:
2	chr3:119219516..119223386-chr3:119224346..119229091,6	K562	blood:
3	chr3:119215837..119219388-chr3:119224900..119228686,9	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD80-1	chr3:119228579-119230323	ENSG00000249939

Variant related genes	Relation type
ENSG00000272662	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000176142	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1060569	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1919586	0.86[AMR][1000 genomes]
rs1919590	0.85[AMR][1000 genomes]
rs1967621	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1976919	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2177812	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687855	0.81[AMR][1000 genomes]
rs4688005	0.90[AMR][1000 genomes]
rs4688007	0.89[AMR][1000 genomes]
rs4688008	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4688012	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6414283	0.90[AMR][1000 genomes]
rs6438529	0.85[AMR][1000 genomes]
rs6438530	0.86[AMR][1000 genomes]
rs6438531	0.88[AMR][1000 genomes]
rs6438535	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6794822	0.80[ASN][1000 genomes]
rs6796970	0.85[AMR][1000 genomes]
rs7621259	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7628626	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7642502	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9809155	0.82[AMR][1000 genomes]
rs9836326	0.83[AMR][1000 genomes]
rs9836627	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9873196	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9877854	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking 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	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119218000-119231800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:119218000-119236600	Weak transcription	Aorta	Aorta
3	chr3:119218600-119231800	Weak transcription	Spleen	Spleen
4	chr3:119218600-119234400	Weak transcription	Colonic Mucosa	Colon
5	chr3:119218600-119236600	Weak transcription	Esophagus	oesophagus
6	chr3:119218800-119233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:119219000-119235800	Weak transcription	Fetal Kidney	kidney
8	chr3:119219400-119236800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:119219600-119237000	Weak transcription	Small Intestine	intestine
10	chr3:119219800-119231000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:119219800-119232000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:119219800-119232000	Weak transcription	Brain Substantia Nigra	brain
13	chr3:119219800-119233600	Weak transcription	Ovary	ovary
14	chr3:119219800-119235800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:119219800-119239200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:119220000-119231800	Weak transcription	Fetal Brain Male	brain
17	chr3:119220000-119243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:119220200-119229200	Weak transcription	HepG2	liver
19	chr3:119220200-119231800	Weak transcription	Fetal Heart	heart
20	chr3:119220200-119246800	Weak transcription	Stomach Mucosa	stomach
21	chr3:119220600-119230600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:119220800-119243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:119221000-119231000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:119221000-119244600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:119221200-119243600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr3:119221200-119244400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:119221400-119245400	Strong transcription	Placenta	Placenta
28	chr3:119221600-119230600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:119221600-119237400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:119221600-119244600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:119221800-119230600	Strong transcription	Dnd41	blood
32	chr3:119221800-119231200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:119222000-119245400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr3:119223200-119233000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:119223400-119229200	Weak transcription	NH-A	brain
36	chr3:119224000-119245200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:119224400-119230000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:119225200-119235000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:119225400-119231800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:119225400-119233400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:119225400-119233600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:119225400-119234000	Weak transcription	Gastric	stomach
43	chr3:119225400-119236000	Weak transcription	Pancreas	Pancrea
44	chr3:119225400-119236600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:119226000-119229600	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:119226000-119233000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr3:119226000-119236800	Weak transcription	Right Ventricle	heart
48	chr3:119226000-119245200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:119226000-119245200	Strong transcription	Liver	Liver
50	chr3:119226600-119229200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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