Variant report

Variant	rs2269684
Chromosome Location	chr12:51417758-51417759
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51417420..51423779-chr12:51473917..51478493,9	MCF-7	breast:
2	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
3	chr12:51404460..51409575-chr12:51416331..51420356,8	MCF-7	breast:
4	chr12:51416514..51419391-chr12:51663583..51665592,2	MCF-7	breast:
5	chr12:51417478..51420284-chr12:51632474..51634014,2	MCF-7	breast:
6	chr12:51158188..51159927-chr12:51415849..51417938,2	K562	blood:
7	chr12:51155914..51160622-chr12:51417270..51421869,9	K562	blood:
8	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
9	chr12:51398011..51404686-chr12:51416862..51423754,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000170545	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000272028	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1079521	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169627	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11169632	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12304878	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12304921	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12305170	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12306808	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12310511	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12315928	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12316856	0.92[EUR][1000 genomes]
rs12317171	0.86[EUR][1000 genomes]
rs12318464	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17125088	0.83[EUR][1000 genomes]
rs17125116	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17125258	0.84[AMR][1000 genomes]
rs224446	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs224454	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs224568	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs224587	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2269685	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2269686	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs453313	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768869	0.80[AMR][1000 genomes]
rs4768876	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4768941	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768942	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768943	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768944	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768945	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4768948	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55679918	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55871024	0.80[AMR][1000 genomes]
rs56060103	0.84[AMR][1000 genomes]
rs56087503	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56335028	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56353532	0.80[AMR][1000 genomes]
rs56402416	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58999537	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59546367	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61005916	0.80[AMR][1000 genomes]
rs61577980	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66518563	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66744607	0.86[EUR][1000 genomes]
rs67106267	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67420027	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67646958	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67654320	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67669227	0.85[EUR][1000 genomes]
rs73090629	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73090631	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73090647	0.89[EUR][1000 genomes]
rs73090649	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73090660	0.80[AMR][1000 genomes]
rs73090661	0.80[AMR][1000 genomes]
rs73090666	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73092531	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73092534	0.80[AMR][1000 genomes]
rs73092537	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73103154	0.84[AMR][1000 genomes]
rs73295896	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73310020	0.86[EUR][1000 genomes]
rs7397054	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7397068	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7973904	0.86[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2269684	TFCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51399200-51418000	Weak transcription	Gastric	stomach
2	chr12:51401400-51417800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:51402000-51418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:51402000-51418000	Weak transcription	Fetal Stomach	stomach
5	chr12:51402400-51418000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:51403000-51418000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:51404800-51417800	Weak transcription	Fetal Brain Female	brain
8	chr12:51407000-51418000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:51410800-51418400	Weak transcription	Primary B cells from cord blood	blood
10	chr12:51412200-51417800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:51412600-51418400	Enhancers	Primary hematopoietic stem cells	blood
12	chr12:51412800-51417800	Enhancers	Brain Cingulate Gyrus	brain
13	chr12:51412800-51418000	Enhancers	Primary T cells from cord blood	blood
14	chr12:51413200-51418400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:51413800-51418000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr12:51414400-51418000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr12:51415000-51417800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:51415400-51418200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:51415800-51417800	Enhancers	Duodenum Mucosa	Duodenum
20	chr12:51416000-51417800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:51416000-51417800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:51416000-51417800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:51416000-51418000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr12:51416000-51418000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:51416000-51419400	Weak transcription	Spleen	Spleen
26	chr12:51416200-51417800	Weak transcription	Right Atrium	heart
27	chr12:51416200-51418200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:51416200-51418400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:51416400-51417800	Weak transcription	Fetal Heart	heart
30	chr12:51416600-51417800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:51416800-51417800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:51416800-51417800	Genic enhancers	Fetal Thymus	thymus
33	chr12:51416800-51417800	Weak transcription	A549	lung
34	chr12:51416800-51418000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr12:51416800-51418000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:51416800-51418000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr12:51417000-51417800	Enhancers	Fetal Kidney	kidney
38	chr12:51417000-51418000	Enhancers	Brain Germinal Matrix	brain
39	chr12:51417000-51418000	Enhancers	Placenta	Placenta
40	chr12:51417000-51418000	Enhancers	Pancreas	Pancrea
41	chr12:51417000-51418000	Enhancers	Psoas Muscle	Psoas
42	chr12:51417000-51418000	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr12:51417000-51418400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:51417000-51418400	Enhancers	Fetal Muscle Leg	muscle
45	chr12:51417200-51417800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr12:51417200-51417800	Enhancers	Brain Angular Gyrus	brain
47	chr12:51417200-51417800	Flanking Active TSS	K562	blood
48	chr12:51417200-51418000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr12:51417200-51418000	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr12:51417200-51418000	Enhancers	Stomach Mucosa	stomach

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