Variant report

Variant	rs2820930
Chromosome Location	chr9:7177945-7177946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM4C-3	chr9:7177838-7178166	XLOC_007276
2	lnc-KDM4C-3	chr9:7177450-7178166	XLOC_007276

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1011341	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs1041288	0.84[AMR][1000 genomes]
rs10511462	0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs10758842	0.90[AMR][1000 genomes]
rs10815533	0.91[ASN][1000 genomes]
rs10815534	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10976118	0.87[AMR][1000 genomes]
rs10976119	0.87[AMR][1000 genomes]
rs1887870	0.86[AMR][1000 genomes]
rs1887871	0.95[ASN][1000 genomes]
rs1887872	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1928211	0.88[AMR][1000 genomes]
rs1928212	0.94[ASN][1000 genomes]
rs1958344	0.95[ASN][1000 genomes]
rs2011128	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2014332	0.89[AMR][1000 genomes]
rs2026709	0.93[ASN][1000 genomes]
rs2094613	0.90[ASN][1000 genomes]
rs2381570	0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2381571	0.86[AMR][1000 genomes]
rs2494241	0.84[AMR][1000 genomes]
rs2494242	0.81[AMR][1000 genomes]
rs2770728	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2770729	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2770730	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2770731	0.95[ASN][1000 genomes]
rs2770732	0.97[ASN][1000 genomes]
rs2770733	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2770734	0.93[ASN][1000 genomes]
rs2770736	0.93[ASN][1000 genomes]
rs2770741	0.95[ASN][1000 genomes]
rs2770742	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2770743	0.96[ASN][1000 genomes]
rs2770744	0.93[ASN][1000 genomes]
rs2770745	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2770746	0.88[ASN][1000 genomes]
rs2770747	0.88[ASN][1000 genomes]
rs2770756	0.87[AMR][1000 genomes]
rs2770760	0.87[AMR][1000 genomes]
rs2820910	0.87[AMR][1000 genomes]
rs2820918	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2820919	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2820920	0.95[ASN][1000 genomes]
rs2820923	0.93[ASN][1000 genomes]
rs2820924	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2820925	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2820926	0.96[ASN][1000 genomes]
rs2820927	0.98[ASN][1000 genomes]
rs2820928	0.98[ASN][1000 genomes]
rs2820929	0.96[ASN][1000 genomes]
rs2820931	0.96[ASN][1000 genomes]
rs2820934	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3753002	0.85[ASN][1000 genomes]
rs3829103	0.89[AMR][1000 genomes]
rs7022054	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs7029684	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7036627	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7874501	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs913584	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs913587	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs913589	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs913590	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs943925	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs971380	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv613259	chr9:7032776-7541338	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1015874	chr9:7048807-7434890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv539971	chr9:7048807-7434890	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv892190	chr9:7094860-7186074	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv892192	chr9:7153009-7257340	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
8	esv2758178	chr9:7175387-7482982	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2759662	chr9:7175387-7482982	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7148600-7185400	Weak transcription	HMEC	breast
2	chr9:7149600-7185400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:7149600-7186200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:7151800-7188600	Weak transcription	Colonic Mucosa	Colon
5	chr9:7160800-7182000	Weak transcription	Dnd41	blood
6	chr9:7162600-7181600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr9:7162600-7182200	Weak transcription	Small Intestine	intestine
8	chr9:7163400-7180600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:7163800-7179000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr9:7164600-7178000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr9:7165800-7179400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr9:7165800-7183800	Weak transcription	Esophagus	oesophagus
13	chr9:7165800-7185400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:7166200-7181000	Weak transcription	Hela-S3	cervix
15	chr9:7167200-7185600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:7169200-7183000	Strong transcription	Primary T cells from cord blood	blood
17	chr9:7171200-7188200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:7171200-7193000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:7172000-7182400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:7172000-7183800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr9:7172600-7185400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr9:7172800-7178600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:7172800-7185400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:7172800-7185400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr9:7172800-7185600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:7173000-7179000	Weak transcription	Brain Angular Gyrus	brain
27	chr9:7173000-7185600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:7173200-7178600	Weak transcription	GM12878-XiMat	blood
29	chr9:7173200-7180200	Weak transcription	HSMMtube	muscle
30	chr9:7173200-7182400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:7173200-7185200	Weak transcription	NHLF	lung
32	chr9:7173200-7185400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:7173400-7179400	Weak transcription	Brain Substantia Nigra	brain
34	chr9:7173400-7185400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:7173400-7185800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr9:7173400-7185800	Weak transcription	Brain Anterior Caudate	brain
37	chr9:7173400-7186200	Weak transcription	Brain Hippocampus Middle	brain
38	chr9:7173400-7186400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr9:7173800-7178000	Strong transcription	Fetal Thymus	thymus
40	chr9:7174400-7179000	Strong transcription	Aorta	Aorta
41	chr9:7175000-7183600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr9:7175000-7191800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:7175200-7178800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr9:7175200-7182000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr9:7175200-7187800	Weak transcription	Ovary	ovary
46	chr9:7176200-7181200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr9:7176200-7183800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr9:7176200-7185400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:7176200-7185400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:7176400-7178000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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