Variant report

Variant	rs2068067
Chromosome Location	chr19:53099308-53099309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53073369..53074894-chr19:53098457..53100751,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF701-1	chr19:53098870-53100598	NONHSAT067565
2	lnc-ZNF701-1	chr19:53099127-53099642	NONHSAT067567
3	lnc-ZNF701-1	chr19:53099127-53099572	NONHSAT067568
4	lnc-ZNF701-1	chr19:53099127-53099572	NONHSAT067566

Variant related genes	Relation type
ENSG00000167562	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10401627	0.88[EUR][1000 genomes]
rs10403603	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420776	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672999	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878446	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11880926	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880939	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11882538	0.92[ASN][1000 genomes]
rs11882556	0.90[ASN][1000 genomes]
rs11883366	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979546	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12985245	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1802617	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2068066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126501	0.91[ASN][1000 genomes]
rs2169527	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2169528	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279151	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279152	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35151776	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35379780	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4450518	0.91[ASN][1000 genomes]
rs4801920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801922	0.93[ASN][1000 genomes]
rs4801923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802975	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802976	0.91[ASN][1000 genomes]
rs60763836	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62117255	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62117256	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509653	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6509654	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509655	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67036527	0.85[ASN][1000 genomes]
rs7245397	0.92[ASN][1000 genomes]
rs7247002	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7247069	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250819	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7254868	0.91[ASN][1000 genomes]
rs7259768	0.92[ASN][1000 genomes]
rs7259905	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7259938	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7260315	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74176156	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110686	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8110794	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv458743	chr19:53065661-53114267	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv580027	chr19:53065661-53114267	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv912304	chr19:53071155-53114267	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1805104	chr19:53090157-53100585	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv963070	chr19:53091108-53105222	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv912305	chr19:53092465-53349850	Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers 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	32 gene(s)	inside rSNPs	diseases
13	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
14	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
15	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	esv2607292	chr19:53094426-53099769	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv3495535	chr19:53095063-53100229	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv828616	chr19:53095216-53137823	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
19	esv1795996	chr19:53099297-53100585	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	esv1827275	chr19:53099297-53103875	Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53074600-53103600	Weak transcription	Fetal Brain Male	brain
2	chr19:53087400-53103600	Weak transcription	Brain Substantia Nigra	brain
3	chr19:53087600-53099400	Weak transcription	Brain Angular Gyrus	brain
4	chr19:53087600-53103600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:53088400-53103600	Weak transcription	Psoas Muscle	Psoas
6	chr19:53088800-53103600	Weak transcription	Colon Smooth Muscle	Colon
7	chr19:53088800-53103600	Weak transcription	Right Ventricle	heart
8	chr19:53088800-53103800	Weak transcription	Right Atrium	heart
9	chr19:53089000-53103800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:53089400-53099400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:53089800-53100000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:53090800-53100000	Weak transcription	Fetal Brain Female	brain
13	chr19:53091000-53104200	Weak transcription	Spleen	Spleen
14	chr19:53091200-53099400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:53091600-53099400	Weak transcription	HSMM	muscle
16	chr19:53092200-53103600	Weak transcription	Gastric	stomach
17	chr19:53094000-53099400	Weak transcription	Brain Germinal Matrix	brain
18	chr19:53094000-53103800	Weak transcription	Aorta	Aorta
19	chr19:53094200-53099400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr19:53095000-53103400	Weak transcription	Fetal Heart	heart
21	chr19:53095200-53099800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr19:53095600-53099800	Weak transcription	NHLF	lung
23	chr19:53095800-53099400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr19:53096000-53103600	Weak transcription	Pancreas	Pancrea
25	chr19:53096000-53103800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr19:53096000-53104000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:53096600-53102200	ZNF genes & repeats	Fetal Intestine Large	intestine
28	chr19:53097400-53100400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
29	chr19:53097600-53099400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:53097600-53100000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:53097600-53100000	ZNF genes & repeats	Thymus	Thymus
32	chr19:53097600-53100200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:53097600-53100200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:53097600-53100200	ZNF genes & repeats	Liver	Liver
35	chr19:53097600-53100400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
36	chr19:53097600-53100400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:53097600-53101000	Strong transcription	Dnd41	blood
38	chr19:53097600-53101200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:53097600-53101200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
40	chr19:53097600-53101200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr19:53097600-53102200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:53097800-53099800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:53097800-53100400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
44	chr19:53097800-53100600	Strong transcription	Placenta	Placenta
45	chr19:53097800-53100800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:53097800-53101000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr19:53097800-53102800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:53098000-53099400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr19:53098000-53099600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:53098000-53099600	Strong transcription	Brain Anterior Caudate	brain

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