Variant report

Variant	rs7133142
Chromosome Location	chr12:117350975-117350976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117348859..117352842-chr12:117353908..117358678,6	K562	blood:
2	chr12:117255053..117257426-chr12:117349302..117351380,2	K562	blood:
3	chr12:117349947..117352255-chr12:117362016..117363854,2	K562	blood:
4	chr12:117349929..117351804-chr12:117393764..117395801,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1032528	0.86[EUR][1000 genomes]
rs1051879	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes]
rs11068246	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11068255	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12099584	0.89[AMR][1000 genomes]
rs12308592	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12316811	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12317604	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12318749	1.00[CEU][hapmap]
rs12321592	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12322695	1.00[MEX][hapmap]
rs16947046	1.00[CEU][hapmap]
rs16947122	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16947131	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16947209	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs16947233	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes]
rs4094199	0.89[AMR][1000 genomes]
rs41364651	0.93[EUR][1000 genomes]
rs4451816	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58882507	0.89[AMR][1000 genomes]
rs59373313	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60272946	0.89[AMR][1000 genomes]
rs61178788	0.89[AMR][1000 genomes]
rs61207925	0.89[AMR][1000 genomes]
rs61288722	0.89[AMR][1000 genomes]
rs7133609	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes]
rs7136880	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7294581	1.00[MEX][hapmap]
rs7302713	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7305313	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7314897	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs73395566	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73395571	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73395601	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73397424	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73397478	0.89[AMR][1000 genomes]
rs73397488	0.89[AMR][1000 genomes]
rs73399480	0.89[AMR][1000 genomes]
rs73399483	0.89[AMR][1000 genomes]
rs73399502	0.89[AMR][1000 genomes]
rs7958175	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7959860	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7963012	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7978853	1.00[MEX][hapmap]
rs884273	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7133142	RNFT2	cis	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117349400-117354400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:117349600-117351000	Enhancers	Small Intestine	intestine
3	chr12:117349600-117351400	Weak transcription	Lung	lung
4	chr12:117349600-117351400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr12:117349600-117352000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr12:117349600-117353800	Weak transcription	Gastric	stomach
7	chr12:117349600-117354200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:117349600-117354200	Weak transcription	Esophagus	oesophagus
9	chr12:117349600-117354400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:117349600-117363600	Weak transcription	Brain Anterior Caudate	brain
11	chr12:117349600-117364000	Weak transcription	Brain Angular Gyrus	brain
12	chr12:117349600-117365800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:117349800-117351200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:117349800-117351200	Enhancers	Primary B cells from peripheral blood	blood
15	chr12:117349800-117351200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr12:117349800-117351200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr12:117349800-117351200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:117349800-117351600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:117349800-117351600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr12:117349800-117353200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:117349800-117353800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr12:117349800-117353800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:117349800-117353800	Weak transcription	NHDF-Ad	bronchial
24	chr12:117349800-117354400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:117349800-117354400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:117349800-117356000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:117349800-117362200	Weak transcription	Thymus	Thymus
28	chr12:117349800-117362400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:117349800-117363600	Weak transcription	Brain Substantia Nigra	brain
30	chr12:117349800-117363800	Weak transcription	Aorta	Aorta
31	chr12:117349800-117364000	Weak transcription	Adipose Nuclei	Adipose
32	chr12:117349800-117366000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr12:117349800-117366000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:117349800-117366000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:117349800-117371000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:117350000-117351200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr12:117350000-117351200	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr12:117350000-117351400	Weak transcription	Fetal Intestine Small	intestine
39	chr12:117350000-117351400	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:117350000-117351400	Weak transcription	HSMM	muscle
41	chr12:117350000-117351600	Enhancers	Dnd41	blood
42	chr12:117350000-117353000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:117350000-117353000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:117350000-117353200	Weak transcription	HMEC	breast
45	chr12:117350000-117353600	Weak transcription	Fetal Brain Female	brain
46	chr12:117350000-117353600	Weak transcription	HSMMtube	muscle
47	chr12:117350000-117353800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:117350000-117353800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:117350000-117353800	Weak transcription	A549	lung
50	chr12:117350000-117354200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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