Variant report

Variant	rs10409380
Chromosome Location	chr19:19307136-19307137
allele	A/C
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	chr19:19307067-19307197	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19305583..19307573-chr19:19309076..19310790,2	K562	blood:
2	chr19:19307070..19310712-chr19:19311051..19314432,7	MCF-7	breast:
3	chr19:19299448..19305567-chr19:19306959..19319217,21	K562	blood:
4	chr19:19305757..19307573-chr19:19308012..19310576,2	K562	blood:

Variant related genes	Relation type
RFXANK	TF binding region
MEF2BNB	TF binding region
MEF2BNB-MEF2B	TF binding region
MEF2B	TF binding region
ENSG00000064489	Chromatin interaction
ENSG00000184162	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000064490	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10401713	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10403193	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409894	0.85[EUR][1000 genomes]
rs10412238	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10424365	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1050483	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2283626	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28618105	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56007657	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73537466	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv933613	chr19:19291456-19312244	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv961283	chr19:19293486-19312277	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription 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	23 gene(s)	inside rSNPs	diseases
6	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19304200-19307600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr19:19304200-19307800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:19304200-19307800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:19304200-19307800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:19304200-19307800	Weak transcription	Aorta	Aorta
6	chr19:19304200-19307800	Weak transcription	Fetal Brain Female	brain
7	chr19:19304200-19307800	Weak transcription	Ovary	ovary
8	chr19:19304200-19313400	Weak transcription	Fetal Kidney	kidney
9	chr19:19304200-19313400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:19304400-19307600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:19304400-19307600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr19:19304400-19307800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:19304600-19307200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr19:19304600-19307200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:19304600-19307600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:19304600-19307800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr19:19304600-19312600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:19304800-19307200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:19304800-19307800	Weak transcription	Pancreas	Pancrea
20	chr19:19304800-19313000	Weak transcription	Stomach Mucosa	stomach
21	chr19:19304800-19313000	Weak transcription	HSMM	muscle
22	chr19:19304800-19313200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr19:19304800-19313600	Weak transcription	Small Intestine	intestine
24	chr19:19305000-19307200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:19305000-19307600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:19305000-19307600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:19305000-19307600	Weak transcription	Placenta	Placenta
28	chr19:19305000-19307600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:19305000-19307600	Weak transcription	A549	lung
30	chr19:19305000-19307600	Weak transcription	NHLF	lung
31	chr19:19305000-19307600	Weak transcription	Osteobl	bone
32	chr19:19305000-19307800	Weak transcription	Gastric	stomach
33	chr19:19305000-19307800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr19:19305000-19307800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr19:19305000-19310400	Weak transcription	HUVEC	blood vessel
36	chr19:19305000-19311000	Strong transcription	Fetal Thymus	thymus
37	chr19:19305000-19312400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr19:19305000-19312400	Weak transcription	HepG2	liver
39	chr19:19305000-19313400	Weak transcription	Fetal Heart	heart
40	chr19:19305200-19307600	Weak transcription	Brain Angular Gyrus	brain
41	chr19:19305400-19307800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr19:19305400-19308000	Weak transcription	Fetal Lung	lung
43	chr19:19305400-19312400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr19:19305400-19313200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:19305600-19307400	Weak transcription	Spleen	Spleen
46	chr19:19305600-19307400	Weak transcription	Dnd41	blood
47	chr19:19305600-19307600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:19305600-19307600	Weak transcription	Lung	lung
49	chr19:19305600-19307800	Weak transcription	Brain Germinal Matrix	brain
50	chr19:19305600-19307800	Weak transcription	Esophagus	oesophagus

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