Variant report

Variant	rs10880
Chromosome Location	chr19:41128309-41128310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41128256-41128395	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41119884..41122816-chr19:41127370..41130174,2	MCF-7	breast:

Variant related genes	Relation type
LTBP4	TF binding region
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11671971	0.83[ASN][1000 genomes]
rs12610819	0.90[ASN][1000 genomes]
rs2162857	0.83[ASN][1000 genomes]
rs2278242	0.86[ASN][1000 genomes]
rs28580028	0.83[ASN][1000 genomes]
rs3786529	0.90[ASN][1000 genomes]
rs56183542	0.83[ASN][1000 genomes]
rs7367	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
15	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
16	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases
17	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10880	CNTD2	cis	cerebellar cortex	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41106000-41136800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41116600-41137000	Weak transcription	Psoas Muscle	Psoas
3	chr19:41117000-41140200	Weak transcription	Brain Angular Gyrus	brain
4	chr19:41120400-41139800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr19:41120600-41129400	Weak transcription	Pancreas	Pancrea
6	chr19:41120600-41133000	Weak transcription	Fetal Brain Male	brain
7	chr19:41120800-41139200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:41120800-41140200	Weak transcription	Brain Anterior Caudate	brain
9	chr19:41121000-41129400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr19:41121200-41129400	Weak transcription	Right Atrium	heart
11	chr19:41121200-41136400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr19:41121200-41137400	Strong transcription	Fetal Muscle Leg	muscle
13	chr19:41121400-41132600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr19:41121400-41140200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr19:41121600-41128600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:41121800-41129600	Weak transcription	HUVEC	blood vessel
17	chr19:41121800-41136800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:41122000-41130000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr19:41122000-41136800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:41122200-41129200	Strong transcription	Fetal Intestine Small	intestine
21	chr19:41122400-41129400	Strong transcription	Fetal Intestine Large	intestine
22	chr19:41122400-41129400	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr19:41123000-41136800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr19:41123200-41128600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:41123200-41129200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:41123200-41133400	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr19:41123400-41140400	Weak transcription	Liver	Liver
28	chr19:41123800-41128400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr19:41123800-41132600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:41124000-41129200	Weak transcription	Colon Smooth Muscle	Colon
31	chr19:41124000-41133400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:41124200-41133400	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:41124200-41136600	Weak transcription	HSMMtube	muscle
34	chr19:41124400-41129000	Strong transcription	NHEK	skin
35	chr19:41124400-41133000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr19:41124400-41136000	Strong transcription	Ovary	ovary
37	chr19:41124800-41128400	Strong transcription	Colonic Mucosa	Colon
38	chr19:41124800-41130200	Strong transcription	Osteobl	bone
39	chr19:41124800-41134000	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr19:41124800-41136000	Strong transcription	Adipose Nuclei	Adipose
41	chr19:41124800-41136200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr19:41125000-41128400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:41125000-41128400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:41125000-41128800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr19:41125000-41128800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:41125000-41129800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:41125000-41132800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr19:41125000-41135800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:41125200-41128600	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr19:41125200-41129000	Strong transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links