Variant report

Variant	rs7397068
Chromosome Location	chr12:51401904-51401905
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51398011..51404686-chr12:51416862..51423754,14	MCF-7	breast:
2	chr12:51397539..51404278-chr12:51405080..51409503,9	MCF-7	breast:
3	chr12:51400476..51402543-chr12:51413177..51415627,2	K562	blood:

Variant related genes	Relation type
ENSG00000110911	Chromatin interaction
ENSG00000272028	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1079521	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169627	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169632	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12304878	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12304921	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12305170	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12306808	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12310511	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12315928	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12316856	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12317171	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12318464	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17125088	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17125116	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs224446	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs224454	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224568	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs224587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269684	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2269685	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs453313	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4768869	0.89[AMR][1000 genomes]
rs4768876	0.82[AMR][1000 genomes]
rs4768941	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768942	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768943	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768944	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768945	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768948	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55679918	0.82[AMR][1000 genomes]
rs55871024	0.89[AMR][1000 genomes]
rs55987825	0.82[ASN][1000 genomes]
rs56087503	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56303785	0.81[ASN][1000 genomes]
rs56353532	0.89[AMR][1000 genomes]
rs56402416	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58999537	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59546367	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61005916	0.89[AMR][1000 genomes]
rs61577980	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66518563	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66744607	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67106267	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67420027	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67646958	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67654320	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67669227	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73090619	0.85[AMR][1000 genomes]
rs73090629	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73090630	0.85[AMR][1000 genomes]
rs73090631	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73090647	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73090649	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73090660	0.89[AMR][1000 genomes]
rs73090661	0.89[AMR][1000 genomes]
rs73090666	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73092531	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73092534	0.89[AMR][1000 genomes]
rs73092537	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73295896	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73310004	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73310020	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7397054	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7973904	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[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	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
rs7397068	TFCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51380200-51402200	Strong transcription	Primary T cells fromperipheralblood	blood
2	chr12:51381200-51402200	Strong transcription	Fetal Thymus	thymus
3	chr12:51381200-51402200	Weak transcription	Psoas Muscle	Psoas
4	chr12:51381200-51402400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:51381200-51403000	Strong transcription	Fetal Muscle Leg	muscle
6	chr12:51381400-51403000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:51381800-51402400	Strong transcription	Liver	Liver
8	chr12:51382000-51402000	Strong transcription	Fetal Stomach	stomach
9	chr12:51382000-51402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:51385600-51402600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:51386000-51406600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:51386000-51414200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:51386800-51402200	Weak transcription	Right Atrium	heart
14	chr12:51388200-51402000	Strong transcription	Adipose Nuclei	Adipose
15	chr12:51388600-51406600	Weak transcription	Small Intestine	intestine
16	chr12:51389400-51405400	Weak transcription	Esophagus	oesophagus
17	chr12:51390000-51405800	Weak transcription	Stomach Mucosa	stomach
18	chr12:51390800-51402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:51391000-51402200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr12:51392600-51402400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr12:51393000-51402000	Strong transcription	Fetal Muscle Trunk	muscle
22	chr12:51393400-51402000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:51394400-51402400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:51394400-51403600	Weak transcription	Ovary	ovary
25	chr12:51395200-51402400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:51395400-51402600	Weak transcription	Fetal Brain Male	brain
27	chr12:51396000-51402200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:51396000-51402400	Strong transcription	Left Ventricle	heart
29	chr12:51396800-51402400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:51397400-51403000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:51397600-51402000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:51397600-51402200	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:51397600-51402400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:51397800-51402200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr12:51397800-51402400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:51398000-51402200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:51398000-51402400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:51398000-51402400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:51398000-51402400	Strong transcription	Dnd41	blood
40	chr12:51398200-51402000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:51398200-51402000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr12:51398200-51402400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:51398200-51402400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:51398200-51402600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:51398400-51402400	Strong transcription	Fetal Lung	lung
46	chr12:51398800-51402600	Weak transcription	Fetal Heart	heart
47	chr12:51398800-51403000	Weak transcription	Colonic Mucosa	Colon
48	chr12:51399000-51403600	Weak transcription	NHLF	lung
49	chr12:51399000-51406200	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:51399200-51402800	Weak transcription	H9 Cell Line	embryonic stem cell

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