Variant report

Variant	rs11671696
Chromosome Location	chr19:19108375-19108376
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	chr19:19108229-19108508	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:19108082-19108497	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19106780..19109822-chr19:19115561..19117365,3	MCF-7	breast:
2	chr19:19106312..19108383-chr19:19109496..19112233,3	MCF-7	breast:
3	chr19:19029943..19032280-chr19:19106563..19108404,2	K562	blood:

Variant related genes	Relation type
SUGP2	TF binding region
ENSG00000105669	Chromatin interaction
ENSG00000105671	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10403272	0.89[ASN][1000 genomes]
rs1079543	0.85[AMR][1000 genomes]
rs11085249	1.00[ASN][1000 genomes]
rs11878368	0.80[AMR][1000 genomes]
rs12016	0.82[AMR][1000 genomes]
rs12975754	0.82[AMR][1000 genomes]
rs1859267	0.80[AMR][1000 genomes]
rs2013813	0.95[ASN][1000 genomes]
rs2269869	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3180770	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4808172	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808176	0.95[ASN][1000 genomes]
rs4808895	1.00[ASN][1000 genomes]
rs4808900	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808904	0.82[AMR][1000 genomes]
rs4808905	0.82[AMR][1000 genomes]
rs4808906	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4808917	0.89[ASN][1000 genomes]
rs6511011	0.81[AFR][1000 genomes]
rs7252615	0.91[ASN][1000 genomes]
rs8111635	0.85[AMR][1000 genomes]
rs9676917	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv2435	chr19:19077432-19122579	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11671696	TMEM161A	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19098600-19109800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:19100200-19117400	Strong transcription	Fetal Intestine Small	intestine
3	chr19:19100600-19122800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:19101000-19109400	Strong transcription	Lung	lung
5	chr19:19101000-19109800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr19:19101000-19114000	Weak transcription	Small Intestine	intestine
7	chr19:19101000-19125600	Strong transcription	Thymus	Thymus
8	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
9	chr19:19101200-19108400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr19:19101200-19108400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:19101200-19109400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:19101200-19109800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr19:19101200-19109800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:19101200-19110400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:19101200-19126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:19101200-19130400	Strong transcription	Duodenum Mucosa	Duodenum
17	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr19:19101400-19109800	Strong transcription	Liver	Liver
19	chr19:19101400-19113000	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr19:19101400-19130400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr19:19101600-19109400	Strong transcription	Adipose Nuclei	Adipose
23	chr19:19101600-19130400	Strong transcription	Primary T cells from cord blood	blood
24	chr19:19101600-19130400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:19101800-19109600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:19101800-19109600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr19:19101800-19109600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:19102000-19110000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr19:19102000-19113000	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr19:19102000-19130200	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr19:19102000-19132000	Strong transcription	Dnd41	blood
32	chr19:19102200-19108400	Strong transcription	Aorta	Aorta
33	chr19:19102200-19110400	Strong transcription	Gastric	stomach
34	chr19:19102400-19109800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr19:19102400-19111000	Strong transcription	A549	lung
36	chr19:19102600-19122600	Weak transcription	Fetal Heart	heart
37	chr19:19102800-19108400	Strong transcription	Right Ventricle	heart
38	chr19:19102800-19109400	Strong transcription	Spleen	Spleen
39	chr19:19103200-19130200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:19103600-19109600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:19103600-19123600	Strong transcription	HepG2	liver
42	chr19:19104000-19114000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr19:19105000-19109800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr19:19105200-19110000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:19105400-19108800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr19:19105400-19108800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr19:19105400-19110600	Weak transcription	Psoas Muscle	Psoas
48	chr19:19105600-19109800	Weak transcription	K562	blood
49	chr19:19105600-19112000	Weak transcription	Colon Smooth Muscle	Colon
50	chr19:19105600-19112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links