Variant report

Variant	rs17125346
Chromosome Location	chr12:51471152-51471153
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51441202..51443113-chr12:51468336..51471322,2	K562	blood:
2	chr12:51470174..51472582-chr12:51632362..51634494,2	K562	blood:
3	chr12:51468579..51474515-chr12:51475298..51478642,16	K562	blood:

Variant related genes	Relation type
ENSG00000183283	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1079521	0.82[AMR][1000 genomes]
rs11169689	0.81[CEU][hapmap]
rs11169691	0.81[CEU][hapmap]
rs12305170	0.95[CHB][hapmap]
rs12317171	0.95[CHB][hapmap]
rs12580097	0.96[EUR][1000 genomes]
rs12582592	1.00[CEU][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs17122760	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs17125258	0.86[CEU][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17125286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17125369	0.96[EUR][1000 genomes]
rs17125375	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17125401	1.00[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs224446	0.89[ASW][hapmap];0.95[CHB][hapmap]
rs224568	0.87[ASW][hapmap]
rs2269685	0.82[AMR][1000 genomes]
rs3751275	0.81[CEU][hapmap]
rs3759406	1.00[CEU][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4768876	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4768948	0.89[ASW][hapmap];0.95[CHB][hapmap]
rs55679918	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55864652	0.95[EUR][1000 genomes]
rs55897461	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55987825	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56060103	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56335028	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56847302	0.96[EUR][1000 genomes]
rs60910794	0.96[EUR][1000 genomes]
rs67466786	0.96[EUR][1000 genomes]
rs67478184	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73103154	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73105025	0.96[EUR][1000 genomes]
rs7397054	0.82[AMR][1000 genomes]
rs7979705	0.90[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17125346	TFCP2	cis	lymphoblastoid	seeQTL
rs17125346	TFCP2	Cis_1M	lymphoblastoid	RTeQTL
rs17125346	TFCP2	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51443400-51476000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:51454000-51475400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:51454200-51475600	Weak transcription	Stomach Mucosa	stomach
4	chr12:51459000-51471400	Weak transcription	Fetal Heart	heart
5	chr12:51459000-51475600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:51459800-51475800	Weak transcription	GM12878-XiMat	blood
7	chr12:51461800-51475200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:51462000-51475800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:51462000-51475800	Weak transcription	Pancreas	Pancrea
10	chr12:51462000-51476400	Weak transcription	Gastric	stomach
11	chr12:51462600-51474400	Weak transcription	Fetal Kidney	kidney
12	chr12:51464400-51475800	Weak transcription	HMEC	breast
13	chr12:51464800-51475800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:51465800-51471400	Weak transcription	Fetal Brain Male	brain
15	chr12:51465800-51471800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:51466000-51471400	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:51466000-51471800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:51466000-51475400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:51466000-51475400	Weak transcription	A549	lung
20	chr12:51466200-51471600	Weak transcription	NHDF-Ad	bronchial
21	chr12:51466400-51475600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:51466800-51475800	Weak transcription	Hela-S3	cervix
23	chr12:51467200-51475600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr12:51467200-51475800	Weak transcription	Primary B cells from cord blood	blood
25	chr12:51467400-51476200	Weak transcription	Colonic Mucosa	Colon
26	chr12:51467800-51471400	Weak transcription	HepG2	liver
27	chr12:51467800-51471600	Weak transcription	Ovary	ovary
28	chr12:51467800-51471600	Weak transcription	NH-A	brain
29	chr12:51467800-51471800	Weak transcription	Aorta	Aorta
30	chr12:51467800-51473600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:51467800-51475200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:51467800-51475200	Weak transcription	HUVEC	blood vessel
33	chr12:51467800-51475400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:51467800-51475400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr12:51467800-51475800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:51467800-51475800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr12:51467800-51475800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr12:51467800-51475800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:51467800-51475800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:51467800-51475800	Weak transcription	Liver	Liver
41	chr12:51468000-51471400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:51468000-51471400	Weak transcription	Fetal Brain Female	brain
43	chr12:51468000-51475600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:51468000-51475600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:51468000-51476000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:51468000-51476400	Weak transcription	Esophagus	oesophagus
47	chr12:51468200-51476000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:51468400-51472200	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr12:51468400-51475200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:51468400-51475200	Weak transcription	Fetal Lung	lung

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