Variant report

Variant	rs11516178
Chromosome Location	chr12:123969457-123969458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123874611..123876401-chr12:123967217..123969868,2	K562	blood:

Variant related genes	Relation type
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11497310	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11497313	1.00[ASN][1000 genomes]
rs11507739	1.00[ASN][1000 genomes]
rs11507743	0.87[EUR][1000 genomes]
rs11516174	0.85[EUR][1000 genomes]
rs11516175	0.88[EUR][1000 genomes]
rs11522340	1.00[ASN][1000 genomes]
rs11522341	0.92[EUR][1000 genomes]
rs11522342	0.92[EUR][1000 genomes]
rs11522343	0.91[EUR][1000 genomes]
rs11523309	0.90[EUR][1000 genomes]
rs11534428	1.00[ASN][1000 genomes]
rs11535679	0.89[EUR][1000 genomes]
rs11559494	1.00[ASN][1000 genomes]
rs11560820	1.00[ASN][1000 genomes]
rs13303266	1.00[ASN][1000 genomes]
rs13303358	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28483351	1.00[ASN][1000 genomes]
rs28493578	0.90[EUR][1000 genomes]
rs28613273	1.00[ASN][1000 genomes]
rs28703907	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28728075	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28781570	0.88[EUR][1000 genomes]
rs28829651	1.00[ASN][1000 genomes]
rs28894691	0.84[EUR][1000 genomes]
rs3087496	1.00[ASN][1000 genomes]
rs34031619	1.00[ASN][1000 genomes]
rs35322317	1.00[ASN][1000 genomes]
rs4047517	1.00[ASN][1000 genomes]
rs4078291	1.00[ASN][1000 genomes]
rs4479070	1.00[ASN][1000 genomes]
rs61953496	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6606747	1.00[ASN][1000 genomes]
rs7300562	1.00[ASN][1000 genomes]
rs7315901	1.00[ASN][1000 genomes]
rs73412280	1.00[ASN][1000 genomes]
rs7957839	0.88[EUR][1000 genomes]
rs7975636	1.00[ASN][1000 genomes]
rs7978323	1.00[ASN][1000 genomes]
rs9330649	1.00[ASN][1000 genomes]
rs9330650	1.00[ASN][1000 genomes]
rs9697264	1.00[ASN][1000 genomes]
rs9697330	0.86[EUR][1000 genomes]
rs9697415	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9697423	0.92[EUR][1000 genomes]
rs9697459	1.00[ASN][1000 genomes]
rs9697616	1.00[ASN][1000 genomes]
rs9697628	1.00[ASN][1000 genomes]
rs9697735	1.00[ASN][1000 genomes]
rs9723026	0.87[EUR][1000 genomes]
rs9723192	1.00[ASN][1000 genomes]
rs9723244	0.82[EUR][1000 genomes]
rs9777715	0.88[EUR][1000 genomes]
rs9777813	1.00[ASN][1000 genomes]
rs9777830	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9778112	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11516178	RP11-486O12.2	cis	Thyroid	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123944600-123995600	Weak transcription	Hela-S3	cervix
2	chr12:123944600-124012200	Strong transcription	Fetal Stomach	stomach
3	chr12:123947600-123971800	Strong transcription	Fetal Intestine Small	intestine
4	chr12:123949000-123984400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:123950400-123973000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:123950800-124007600	Weak transcription	Colonic Mucosa	Colon
7	chr12:123954200-123971000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:123955200-123971000	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:123956800-123973400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:123956800-123993400	Weak transcription	HMEC	breast
11	chr12:123956800-123995400	Weak transcription	Fetal Brain Male	brain
12	chr12:123957400-123972800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:123957400-123973000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:123957400-123982400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:123957400-123995400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:123957400-123995400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:123957600-123995400	Weak transcription	Pancreas	Pancrea
18	chr12:123957600-124003800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:123957800-123982600	Weak transcription	A549	lung
20	chr12:123959000-123970400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:123959400-123970600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:123960000-123995400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:123960200-123972200	Weak transcription	Fetal Kidney	kidney
24	chr12:123960200-123973000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:123961400-123969600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:123961600-123973200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:123961600-123979200	Weak transcription	NHEK	skin
28	chr12:123961600-123995800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:123963000-123981200	Weak transcription	Esophagus	oesophagus
30	chr12:123963800-123970400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:123964000-123978600	Weak transcription	Right Atrium	heart
32	chr12:123964200-123978200	Weak transcription	Psoas Muscle	Psoas
33	chr12:123964200-123981200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:123964200-123981200	Weak transcription	Spleen	Spleen
35	chr12:123964200-123981400	Weak transcription	NHDF-Ad	bronchial
36	chr12:123964400-123971000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr12:123964400-123976800	Weak transcription	Fetal Heart	heart
38	chr12:123964400-123981200	Weak transcription	Gastric	stomach
39	chr12:123964600-123973000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:123964600-123973000	Weak transcription	HSMMtube	muscle
41	chr12:123965200-123981000	Weak transcription	Fetal Intestine Large	intestine
42	chr12:123965400-123972600	Strong transcription	Fetal Muscle Leg	muscle
43	chr12:123965400-123981400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr12:123965400-123983000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr12:123965600-123970400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:123965600-123978200	Weak transcription	Aorta	Aorta
47	chr12:123965600-123979400	Weak transcription	HSMM	muscle
48	chr12:123965600-123981200	Weak transcription	NHLF	lung
49	chr12:123965600-123982600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr12:123965800-123969800	Weak transcription	Brain Inferior Temporal Lobe	brain

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