Variant report

Variant	rs11169687
Chromosome Location	chr12:51441118-51441119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:51440789-51443068	HepG2	liver:	n/a	n/a

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
2	chr12:51440622..51443141-chr12:51753837..51755674,2	MCF-7	breast:
3	chr12:51440322..51443098-chr12:51662230..51665433,4	K562	blood:
4	chr12:51440588..51444188-chr12:51475693..51478745,10	K562	blood:
5	chr12:51440271..51447226-chr12:51475135..51479930,16	MCF-7	breast:
6	chr12:51440439..51443022-chr12:51565659..51567306,3	K562	blood:
7	chr12:51418602..51423346-chr12:51439309..51444851,15	MCF-7	breast:
8	chr12:51440619..51442939-chr12:51783521..51786364,2	MCF-7	breast:
9	chr12:51439067..51445190-chr12:51449547..51456560,11	K562	blood:
10	chr12:51440784..51442942-chr12:51664189..51666029,2	MCF-7	breast:
11	chr12:51440111..51442560-chr12:51783834..51785722,2	MCF-7	breast:
12	chr12:51429499..51431522-chr12:51440148..51442114,3	MCF-7	breast:
13	chr12:51440642..51443592-chr12:51616961..51619958,3	MCF-7	breast:
14	chr12:51156477..51159239-chr12:51440349..51444629,5	K562	blood:
15	chr12:51440743..51444863-chr12:51448295..51453075,7	MCF-7	breast:
16	chr12:51440639..51443821-chr12:51630707..51634068,3	K562	blood:
17	chr12:51399373..51401239-chr12:51441069..51443548,3	MCF-7	breast:
18	chr12:51441021..51443304-chr12:51610017..51612719,2	MCF-7	breast:
19	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
20	chr12:51319328..51321939-chr12:51438898..51441573,2	K562	blood:
21	chr12:51440554..51443122-chr12:51610984..51612842,2	K562	blood:
22	chr12:51440782..51445752-chr12:51631445..51635429,5	MCF-7	breast:
23	chr12:51441033..51441729-chr12:51640254..51641009,2	K562	blood:
24	chr12:51440588..51444188-chr12:51475774..51478819,7	K562	blood:
25	chr12:51440852..51445521-chr12:51475730..51478507,6	MCF-7	breast:

No data

Variant related genes	Relation type
LETMD1	TF binding region
ENSG00000110911	Chromatin interaction
ENSG00000135457	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000050438	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000199903	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000184271	Chromatin interaction
ENSG00000139629	Chromatin interaction
ENSG00000269339	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10876133	0.82[AMR][1000 genomes]
rs11169674	0.80[AMR][1000 genomes]
rs11169675	0.80[AMR][1000 genomes]
rs11169681	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169700	0.91[AMR][1000 genomes]
rs11169706	0.82[AMR][1000 genomes]
rs11169708	0.82[AMR][1000 genomes]
rs12312531	0.80[AMR][1000 genomes]
rs17125363	0.82[AMR][1000 genomes]
rs17125365	0.91[AMR][1000 genomes]
rs17125371	0.82[AMR][1000 genomes]
rs2269682	0.80[AMR][1000 genomes]
rs2269683	0.80[AMR][1000 genomes]
rs3809320	0.80[AMR][1000 genomes]
rs4768953	0.82[AMR][1000 genomes]
rs4768957	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7953765	0.82[AMR][1000 genomes]
rs8490	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51438600-51441400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:51440600-51441200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr12:51440600-51441200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:51440600-51441200	Enhancers	Brain Cingulate Gyrus	brain
5	chr12:51440600-51441200	Enhancers	Colon Smooth Muscle	Colon
6	chr12:51440600-51441400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr12:51440800-51441200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:51440800-51441200	Enhancers	Primary B cells from cord blood	blood
9	chr12:51440800-51441200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr12:51440800-51441200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:51440800-51441200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:51440800-51441200	Enhancers	Adipose Nuclei	Adipose
13	chr12:51440800-51441200	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr12:51440800-51441200	Enhancers	Brain Substantia Nigra	brain
15	chr12:51440800-51441200	Enhancers	Duodenum Mucosa	Duodenum
16	chr12:51440800-51441200	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr12:51440800-51441200	Enhancers	HMEC	breast
18	chr12:51440800-51441200	Flanking Active TSS	K562	blood
19	chr12:51440800-51441400	Enhancers	Primary B cells from peripheral blood	blood
20	chr12:51440800-51441400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr12:51440800-51441400	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr12:51440800-51441400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr12:51440800-51441400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:51440800-51441400	Enhancers	Fetal Heart	heart
25	chr12:51440800-51441400	Enhancers	Fetal Intestine Small	intestine
26	chr12:51440800-51441400	Enhancers	Fetal Lung	lung
27	chr12:51440800-51441400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr12:51440800-51441600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:51440800-51441600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr12:51440800-51441600	Flanking Active TSS	Dnd41	blood
31	chr12:51440800-51442600	Active TSS	Stomach Smooth Muscle	stomach
32	chr12:51440800-51442800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:51441000-51441200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:51441000-51441200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:51441000-51441200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:51441000-51441200	Enhancers	Muscle Satellite Cultured Cells	--
37	chr12:51441000-51441200	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr12:51441000-51441200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:51441000-51441200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:51441000-51441200	Enhancers	Brain Hippocampus Middle	brain
41	chr12:51441000-51441200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:51441000-51441200	Enhancers	Colonic Mucosa	Colon
43	chr12:51441000-51441200	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr12:51441000-51441200	Enhancers	Fetal Muscle Trunk	muscle
45	chr12:51441000-51441200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr12:51441000-51441200	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr12:51441000-51441200	Flanking Active TSS	Hela-S3	cervix
48	chr12:51441000-51441200	Flanking Active TSS	HepG2	liver
49	chr12:51441000-51441200	Enhancers	NHEK	skin
50	chr12:51441000-51441400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links