Variant report

Variant	rs12050099
Chromosome Location	chr14:55764331-55764332
allele	C/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	NFIC	chr14:55764312-55764909	ECC-1	luminal epithelium:	n/a	chr14:55764514-55764530
2	NFIC	chr14:55764171-55764986	ECC-1	luminal epithelium:	n/a	chr14:55764514-55764530

No.	Distal block	Cell Line	Cell type
1	chr14:55737517..55738470-chr14:55763647..55765215,7	MCF-7	breast:
2	chr14:55737321..55738465-chr14:55764329..55765201,4	MCF-7	breast:
3	chr14:55764219..55765273-chr14:55820714..55821903,4	MCF-7	breast:
4	chr14:55736930..55738808-chr14:55763982..55767802,4	MCF-7	breast:
5	chr14:55748156..55749852-chr14:55763544..55765374,2	K562	blood:
6	chr14:55747623..55750356-chr14:55762844..55765172,2	MCF-7	breast:

Variant related genes	Relation type
CHMP4BP1	TF binding region
ENSG00000178974	Chromatin interaction
ENSG00000258413	Chromatin interaction
ENSG00000239686	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10129505	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10131562	0.82[ASN][1000 genomes]
rs10131730	0.83[ASN][1000 genomes]
rs10131913	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10131926	0.86[EUR][1000 genomes]
rs10132453	0.83[ASN][1000 genomes]
rs10134317	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10136596	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10137307	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10139000	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10139083	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10139337	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10139678	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10139683	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10140063	0.95[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10140801	0.93[EUR][1000 genomes]
rs10140869	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10141396	0.84[ASN][1000 genomes]
rs10141483	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10141552	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10142448	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10142547	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10142803	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10142823	0.89[EUR][1000 genomes]
rs10143136	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10144418	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10145203	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10146637	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10147765	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10150699	0.89[EUR][1000 genomes]
rs10150760	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1045002	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10467798	0.88[EUR][1000 genomes]
rs1109170	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11158034	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11158037	0.83[ASN][1000 genomes]
rs11547116	0.90[EUR][1000 genomes]
rs11625001	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11625423	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11626751	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11628437	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11848456	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11848575	0.99[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11851169	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12050123	0.83[ASN][1000 genomes]
rs13379169	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1572611	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17674463	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17674563	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17740551	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17740741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17741542	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17741831	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1952087	0.84[EUR][1000 genomes]
rs1972221	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2016931	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2026633	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2209808	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2297816	0.83[ASN][1000 genomes]
rs2341621	0.89[EUR][1000 genomes]
rs2341622	0.89[EUR][1000 genomes]
rs28428911	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28430823	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28452705	0.82[ASN][1000 genomes]
rs28493647	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28504448	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28568813	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28612464	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28660594	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2880103	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs35112084	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3742569	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3783648	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3783649	0.82[ASN][1000 genomes]
rs3783651	0.82[ASN][1000 genomes]
rs3783652	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4366639	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4496026	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4580079	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56166765	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs56949365	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58260073	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58296156	0.83[ASN][1000 genomes]
rs58458194	0.99[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs59629906	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59871474	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60248556	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61210954	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6573009	0.84[EUR][1000 genomes]
rs6573010	0.86[EUR][1000 genomes]
rs6573014	0.90[EUR][1000 genomes]
rs66464079	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs66551709	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs66696758	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67386901	0.99[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs67412516	0.82[ASN][1000 genomes]
rs67514154	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67795323	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs67822108	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs68046603	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68138420	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7140628	0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7142857	0.85[EUR][1000 genomes]
rs7144292	0.83[EUR][1000 genomes]
rs7144737	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7146748	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7146752	0.90[EUR][1000 genomes]
rs7147136	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7147247	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7148171	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7150234	0.89[ASN][1000 genomes]
rs7150763	0.83[ASN][1000 genomes]
rs7151581	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7151754	0.96[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7152390	0.85[ASN][1000 genomes]
rs7153612	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7153645	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7154796	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7154831	0.83[ASN][1000 genomes]
rs7155954	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7157308	0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7158768	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7158791	0.83[ASN][1000 genomes]
rs7158861	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7159824	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7161439	0.82[ASN][1000 genomes]
rs72715769	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72717738	0.82[ASN][1000 genomes]
rs73263927	0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8005450	0.89[ASN][1000 genomes]
rs8008119	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8011288	0.94[EUR][1000 genomes]
rs8013713	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8014477	0.83[ASN][1000 genomes]
rs8014540	0.83[ASN][1000 genomes]
rs8015211	0.83[ASN][1000 genomes]
rs8021583	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8022225	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs943590	0.91[EUR][1000 genomes]
rs9919923	0.84[ASN][1000 genomes]
rs9919926	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9919932	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039438	chr14:55746585-55886099	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12050099	RP11-665C16.6	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55739200-55768400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr14:55740000-55770600	Weak transcription	Colonic Mucosa	Colon
3	chr14:55741000-55764600	Weak transcription	Fetal Muscle Leg	muscle
4	chr14:55741000-55773200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr14:55741800-55764600	Weak transcription	HMEC	breast
6	chr14:55742000-55765400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr14:55744000-55767800	Weak transcription	K562	blood
8	chr14:55744800-55764800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr14:55744800-55765400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr14:55744800-55767800	Weak transcription	Pancreas	Pancrea
11	chr14:55745000-55768400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr14:55745000-55774000	Weak transcription	Liver	Liver
13	chr14:55745200-55778400	Weak transcription	Fetal Thymus	thymus
14	chr14:55745600-55764400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr14:55745600-55769200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr14:55745800-55765400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr14:55745800-55765400	Weak transcription	Fetal Stomach	stomach
18	chr14:55747400-55768400	Weak transcription	NHLF	lung
19	chr14:55748000-55770000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr14:55749400-55769800	Weak transcription	Primary B cells from cord blood	blood
21	chr14:55751600-55765200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr14:55752000-55765200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr14:55752000-55765400	Weak transcription	Fetal Intestine Small	intestine
24	chr14:55752200-55764400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr14:55752200-55765200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr14:55752200-55765200	Weak transcription	Lung	lung
27	chr14:55752600-55768200	Weak transcription	HSMM	muscle
28	chr14:55752800-55764600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr14:55754400-55768400	Weak transcription	NHDF-Ad	bronchial
30	chr14:55754600-55764600	Weak transcription	Adipose Nuclei	Adipose
31	chr14:55754800-55765200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr14:55754800-55778800	Weak transcription	Hela-S3	cervix
33	chr14:55755000-55770600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr14:55755000-55774800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr14:55755200-55768000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr14:55755800-55768400	Weak transcription	Fetal Brain Female	brain
37	chr14:55756400-55779000	Weak transcription	Gastric	stomach
38	chr14:55757000-55765400	Weak transcription	Right Ventricle	heart
39	chr14:55757000-55767000	Weak transcription	Psoas Muscle	Psoas
40	chr14:55757400-55764400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr14:55758800-55769600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr14:55759400-55768600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr14:55760200-55764600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr14:55760200-55765200	Weak transcription	Esophagus	oesophagus
45	chr14:55760200-55765400	Weak transcription	HepG2	liver
46	chr14:55760400-55768400	Weak transcription	Colon Smooth Muscle	Colon
47	chr14:55761200-55768400	Weak transcription	Ovary	ovary
48	chr14:55761200-55773200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr14:55761400-55765400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr14:55761600-55765200	Weak transcription	Thymus	Thymus

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