Variant report

Variant	rs56303785
Chromosome Location	chr12:51329938-51329939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51329075..51331156-chr12:51335515..51338529,3	MCF-7	breast:
2	chr12:51155577..51158577-chr12:51327388..51330247,3	MCF-7	breast:
3	chr12:51233571..51235108-chr12:51328091..51331063,2	K562	blood:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11169627	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169632	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12304878	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12304921	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12305170	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12306808	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12310511	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12315928	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12316856	0.89[ASN][1000 genomes]
rs12317171	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12318464	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17125088	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17125116	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs224446	0.83[ASN][1000 genomes]
rs224587	0.80[ASN][1000 genomes]
rs4768941	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768942	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768943	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768944	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768945	0.91[ASN][1000 genomes]
rs4768948	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56087503	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56402416	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58999537	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59546367	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61577980	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66518563	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66744607	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67106267	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67420027	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67646958	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67654320	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67669227	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73090629	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73090631	0.88[EUR][1000 genomes]
rs73090647	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73090649	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73090666	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73092531	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73092537	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73295896	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73310004	0.88[ASN][1000 genomes]
rs73310020	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7397068	0.81[ASN][1000 genomes]
rs7973904	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[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
rs56303785	TFCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51319400-51346200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51320200-51330600	Weak transcription	Primary T cells from cord blood	blood
3	chr12:51322200-51332600	Weak transcription	Fetal Kidney	kidney
4	chr12:51322800-51331800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:51323000-51331000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
7	chr12:51323400-51330000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:51323400-51330800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:51323400-51330800	Weak transcription	Brain Germinal Matrix	brain
10	chr12:51323400-51330800	Weak transcription	Fetal Brain Female	brain
11	chr12:51324200-51331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:51324400-51331200	Enhancers	Stomach Mucosa	stomach
13	chr12:51324600-51331000	Weak transcription	Lung	lung
14	chr12:51325400-51331000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:51326400-51331000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr12:51327200-51330800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:51327200-51331400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr12:51327400-51331400	Weak transcription	Colonic Mucosa	Colon
19	chr12:51327400-51331400	Enhancers	Placenta	Placenta
20	chr12:51327600-51331400	Weak transcription	Brain Angular Gyrus	brain
21	chr12:51327800-51331000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:51327800-51331000	Weak transcription	Thymus	Thymus
23	chr12:51327800-51331200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:51327800-51331200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:51328000-51331000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:51328000-51331000	Weak transcription	Brain Anterior Caudate	brain
27	chr12:51328000-51331000	Weak transcription	Pancreas	Pancrea
28	chr12:51328000-51331200	Weak transcription	Fetal Lung	lung
29	chr12:51328200-51330400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:51328400-51331000	Weak transcription	Primary B cells from cord blood	blood
31	chr12:51328400-51331000	Weak transcription	Gastric	stomach
32	chr12:51328400-51332600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:51328600-51330800	Weak transcription	Fetal Muscle Leg	muscle
34	chr12:51328800-51330200	Weak transcription	K562	blood
35	chr12:51328800-51330400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr12:51328800-51378000	Weak transcription	Brain Substantia Nigra	brain
37	chr12:51329000-51331200	Enhancers	Primary hematopoietic stem cells	blood
38	chr12:51329200-51331200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr12:51329200-51331400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:51329200-51331400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:51329200-51336200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:51329200-51341600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:51329400-51330600	Enhancers	Liver	Liver
44	chr12:51329400-51330600	Enhancers	HepG2	liver
45	chr12:51329400-51330800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:51329400-51330800	Weak transcription	HMEC	breast
47	chr12:51329400-51331000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:51329400-51331000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:51329400-51331000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:51329400-51331000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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