Variant report

Variant	rs17125258
Chromosome Location	chr12:51445679-51445680
allele	A/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	RCOR1	chr12:51445653-51445946	K562	blood:	n/a	n/a
2	POLR2A	chr12:51445449-51445978	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr12:51445478-51446081	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51440271..51447226-chr12:51475135..51479930,16	MCF-7	breast:
2	chr12:51445541..51448064-chr12:51474329..51477358,3	MCF-7	breast:
3	chr12:51440782..51445752-chr12:51631445..51635429,5	MCF-7	breast:
4	chr12:51444294..51447069-chr12:51453786..51456012,3	MCF-7	breast:

Variant related genes	Relation type
LETMD1	TF binding region
ENSG00000110925	Chromatin interaction
ENSG00000183283	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1079521	0.80[AMR][1000 genomes]
rs12580097	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12582592	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17125286	0.86[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17125346	0.86[CEU][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17125369	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17125375	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17125401	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs224454	0.82[AMR][1000 genomes]
rs224568	0.95[CHB][hapmap]
rs2269684	0.84[AMR][1000 genomes]
rs2269685	0.80[AMR][1000 genomes]
rs3759406	0.86[CEU][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4768876	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55679918	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55864652	0.94[EUR][1000 genomes]
rs55897461	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55987825	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56060103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56335028	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56847302	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60910794	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67466786	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73103154	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73105025	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7397054	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7979705	1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[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
rs17125258	TFCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51442800-51448200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51442800-51449000	Weak transcription	Aorta	Aorta
3	chr12:51442800-51449800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:51442800-51450000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:51442800-51452800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:51442800-51470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:51443000-51447000	Weak transcription	Lung	lung
8	chr12:51443000-51448200	Weak transcription	Gastric	stomach
9	chr12:51443000-51453200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:51443200-51447200	Weak transcription	Ovary	ovary
11	chr12:51443200-51447600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:51443200-51449600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:51443400-51445800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:51443400-51447000	Weak transcription	Spleen	Spleen
15	chr12:51443400-51447200	Weak transcription	Pancreas	Pancrea
16	chr12:51443400-51447400	Weak transcription	HSMM	muscle
17	chr12:51443400-51447600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:51443400-51448200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:51443400-51448200	Weak transcription	Esophagus	oesophagus
20	chr12:51443400-51449200	Weak transcription	Right Ventricle	heart
21	chr12:51443400-51452600	Weak transcription	Stomach Mucosa	stomach
22	chr12:51443400-51476000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:51443600-51447000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:51443600-51447200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:51443600-51447400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:51443600-51447400	Weak transcription	Primary B cells from cord blood	blood
27	chr12:51443600-51447600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:51443600-51447800	Weak transcription	Brain Angular Gyrus	brain
29	chr12:51443600-51448600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:51443600-51451600	Weak transcription	Colonic Mucosa	Colon
31	chr12:51443600-51451800	Weak transcription	Small Intestine	intestine
32	chr12:51443600-51452600	Weak transcription	Psoas Muscle	Psoas
33	chr12:51443600-51457400	Weak transcription	Fetal Brain Male	brain
34	chr12:51443600-51459600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr12:51443600-51462800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:51443800-51445800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:51443800-51445800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:51443800-51445800	Weak transcription	Fetal Brain Female	brain
39	chr12:51443800-51446000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:51443800-51446000	Weak transcription	HMEC	breast
41	chr12:51443800-51446600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:51443800-51447000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:51443800-51447400	Weak transcription	Fetal Lung	lung
44	chr12:51443800-51447800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:51443800-51448000	Weak transcription	NHLF	lung
46	chr12:51443800-51449000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr12:51443800-51455600	Weak transcription	Fetal Heart	heart
48	chr12:51443800-51462600	Strong transcription	A549	lung
49	chr12:51444000-51445800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr12:51444000-51449600	Weak transcription	HUVEC	blood vessel

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