Variant report

Variant	rs11661718
Chromosome Location	chr18:29621121-29621122
allele	A/G
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	MXI1	chr18:29621056-29621153	GM12878	blood:	n/a	n/a
2	GATA2	chr18:29620966-29621180	HUVEC	blood vessel:	n/a	chr18:29621088-29621104
3	RUNX3	chr18:29620860-29621224	GM12878	blood:	n/a	n/a
4	MYC	chr18:29620845-29621270	NB4	blood:	n/a	n/a
5	RUNX3	chr18:29620829-29621190	GM12878	blood:	n/a	n/a
6	MAX	chr18:29620902-29621310	NB4	blood:	n/a	n/a
7	GATA3	chr18:29620919-29621149	SH-SY5Y	brain:	n/a	chr18:29621088-29621104
8	POLR2A	chr18:29620751-29621332	HL-60	blood:	n/a	n/a
9	POLR2A	chr18:29620926-29621275	HL-60	blood:	n/a	n/a
10	CHD2	chr18:29621058-29621232	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29616707..29618971-chr18:29620186..29622381,2	K562	blood:

Variant related genes	Relation type
RNF125	TF binding region
ENSG00000101695	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10438934	0.96[ASN][1000 genomes]
rs170861	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs189209	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2006768	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2432697	0.81[ASN][1000 genomes]
rs2432699	0.81[EUR][1000 genomes]
rs2433379	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2433380	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28621808	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2901365	0.81[ASN][1000 genomes]
rs2911636	0.92[ASN][1000 genomes]
rs2912538	0.91[ASN][1000 genomes]
rs336272	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs336275	0.81[ASN][1000 genomes]
rs336276	0.81[ASN][1000 genomes]
rs336280	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35672529	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs373667	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs454768	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4799627	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs606590	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs618790	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs685446	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs686271	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72934872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73413971	0.92[ASN][1000 genomes]
rs8089092	0.80[ASN][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	esv1803283	chr18:29591102-29640430	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
2	nsv1061305	chr18:29609935-29664528	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11661718	RP11-53I6.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29599600-29629600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr18:29600600-29628400	Weak transcription	Hela-S3	cervix
3	chr18:29600800-29632400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr18:29602600-29628600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr18:29602600-29664200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr18:29604600-29656000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr18:29606800-29637000	Weak transcription	Brain Anterior Caudate	brain
8	chr18:29609800-29628600	Weak transcription	Small Intestine	intestine
9	chr18:29611600-29628800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr18:29611800-29629000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr18:29613000-29627000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr18:29615200-29648400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr18:29615800-29628400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr18:29616000-29640200	Weak transcription	Esophagus	oesophagus
15	chr18:29616200-29628800	Weak transcription	Gastric	stomach
16	chr18:29617200-29629600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr18:29618000-29628800	Weak transcription	Left Ventricle	heart
18	chr18:29618000-29629000	Weak transcription	Lung	lung
19	chr18:29618200-29624400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr18:29618200-29624600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr18:29618400-29639800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr18:29618400-29646800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr18:29618600-29628200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr18:29618600-29628600	Weak transcription	Spleen	Spleen
25	chr18:29618600-29642800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr18:29619000-29622000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr18:29619400-29624400	Weak transcription	Fetal Muscle Leg	muscle
28	chr18:29619400-29624600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr18:29619400-29625600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr18:29619400-29645400	Weak transcription	Fetal Stomach	stomach
31	chr18:29619600-29622000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr18:29619600-29622400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr18:29619800-29622000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr18:29619800-29622800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr18:29620000-29623400	Enhancers	Primary B cells from peripheral blood	blood
36	chr18:29620000-29624600	Weak transcription	Fetal Intestine Small	intestine
37	chr18:29620000-29625800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr18:29620200-29621600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr18:29620200-29622400	Weak transcription	Liver	Liver
40	chr18:29620400-29621200	Enhancers	Fetal Intestine Large	intestine
41	chr18:29620400-29621200	Enhancers	Stomach Mucosa	stomach
42	chr18:29620400-29621200	Flanking Active TSS	Dnd41	blood
43	chr18:29620400-29621400	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr18:29620400-29621400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr18:29620400-29621400	Enhancers	Brain Hippocampus Middle	brain
46	chr18:29620400-29621400	Enhancers	Brain Substantia Nigra	brain
47	chr18:29620400-29621400	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr18:29620400-29621600	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr18:29620400-29621600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr18:29620400-29625000	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links