Variant report

Variant	rs7250969
Chromosome Location	chr19:53100377-53100378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:1 , 50 per page) page: 1

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

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF701-1	chr19:53098870-53100598	NONHSAT067565
2	lnc-ZNF701-1	chr19:53100112-53100660	NONHSAT067567
3	lnc-ZNF701-1	chr19:53100261-53100564	NONHSAT067568
4	lnc-ZNF701-1	chr19:53099937-53100823	NONHSAT067569
5	lnc-ZNF701-1	chr19:53100112-53100660	NONHSAT067566

No data

Variant related genes	Relation type
ENSG00000167562	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16984003	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34202608	1.00[ASN][1000 genomes]
rs34281921	1.00[ASN][1000 genomes]
rs35217466	1.00[ASN][1000 genomes]
rs35265503	1.00[ASN][1000 genomes]
rs35443353	1.00[ASN][1000 genomes]
rs35496699	1.00[ASN][1000 genomes]
rs35512045	1.00[ASN][1000 genomes]
rs58246752	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74176155	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
17	esv1795996	chr19:53099297-53100585	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	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:99 , 50 per page) page: 1 2

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	chr19:53087600-53103600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:53088400-53103600	Weak transcription	Psoas Muscle	Psoas
5	chr19:53088800-53103600	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:53088800-53103600	Weak transcription	Right Ventricle	heart
7	chr19:53088800-53103800	Weak transcription	Right Atrium	heart
8	chr19:53089000-53103800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:53091000-53104200	Weak transcription	Spleen	Spleen
10	chr19:53092200-53103600	Weak transcription	Gastric	stomach
11	chr19:53094000-53103800	Weak transcription	Aorta	Aorta
12	chr19:53095000-53103400	Weak transcription	Fetal Heart	heart
13	chr19:53096000-53103600	Weak transcription	Pancreas	Pancrea
14	chr19:53096000-53103800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:53096000-53104000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:53096600-53102200	ZNF genes & repeats	Fetal Intestine Large	intestine
17	chr19:53097400-53100400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
18	chr19:53097600-53100400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
19	chr19:53097600-53100400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:53097600-53101000	Strong transcription	Dnd41	blood
21	chr19:53097600-53101200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:53097600-53101200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
23	chr19:53097600-53101200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
24	chr19:53097600-53102200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:53097800-53100400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
26	chr19:53097800-53100600	Strong transcription	Placenta	Placenta
27	chr19:53097800-53100800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:53097800-53101000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr19:53097800-53102800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:53098000-53100400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:53098000-53100400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
32	chr19:53098000-53100600	Strong transcription	Adipose Nuclei	Adipose
33	chr19:53098000-53100800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:53098000-53101000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
35	chr19:53098000-53101200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:53098200-53100800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:53098200-53100800	Weak transcription	Lung	lung
38	chr19:53098200-53101000	Strong transcription	Fetal Muscle Leg	muscle
39	chr19:53098200-53103800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:53098400-53100800	Strong transcription	Fetal Thymus	thymus
41	chr19:53098600-53101200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr19:53098800-53100400	Strong transcription	Fetal Kidney	kidney
43	chr19:53098800-53100800	Weak transcription	Fetal Stomach	stomach
44	chr19:53099000-53100400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr19:53099000-53100400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
46	chr19:53099000-53100400	Strong transcription	Fetal Lung	lung
47	chr19:53099000-53100600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr19:53099200-53100400	ZNF genes & repeats	Primary T cells from cord blood	blood
49	chr19:53099200-53100400	Strong transcription	Rectal Smooth Muscle	rectum
50	chr19:53099200-53100600	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links