Variant report

Variant	rs7970990
Chromosome Location	chr12:11325148-11325149
allele	A/T
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	REST	chr12:11323254-11325495	H1-neurons	neurons:	n/a	chr12:11324075-11324088
2	POLR2A	chr12:11323403-11325204	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:11323147-11325377	K562	blood:	n/a	n/a
4	POLR2A	chr12:11323484-11325334	MCF10A-Er-Src	breast:	n/a	n/a
5	HCFC1	chr12:11323329-11325360	Hela-S3	cervix:	n/a	n/a
6	TBP	chr12:11323551-11325221	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:11091072..11093170-chr12:11322389..11325259,3	MCF-7	breast:
2	chr12:10365255..10367563-chr12:11322614..11325373,2	K562	blood:
3	chr12:11322782..11326787-chr12:11332516..11335699,5	K562	blood:
4	chr12:11321748..11327565-chr12:11327784..11333912,14	MCF-7	breast:
5	chr12:10760446..10762203-chr12:11323888..11325802,2	K562	blood:

Variant related genes	Relation type
PRR4	TF binding region
ENSG00000256712	TF binding region
TAS2R14	TF binding region
ENSG00000111196	Chromatin interaction
ENSG00000139112	Chromatin interaction
ENSG00000255958	Chromatin interaction
ENSG00000212127	Chromatin interaction
ENSG00000256629	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11516172	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11522335	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13302964	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1451767	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28542794	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34263586	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34280471	0.85[AFR][1000 genomes]
rs34315443	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34423519	0.82[AFR][1000 genomes]
rs34490574	0.82[AFR][1000 genomes]
rs34808476	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34825996	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34897085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34989493	0.92[EUR][1000 genomes]
rs35034090	0.82[AFR][1000 genomes]
rs35039890	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35641223	0.82[AFR][1000 genomes]
rs35760416	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35860793	0.82[AFR][1000 genomes]
rs35962483	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36057066	0.82[AFR][1000 genomes]
rs3851591	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7135943	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7296803	0.81[AFR][1000 genomes]
rs7299875	0.82[AFR][1000 genomes]
rs73051374	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7959172	0.81[AFR][1000 genomes]
rs7980237	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv1038277	chr12:11060978-11504091	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv898783	chr12:11185236-11338781	ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv898784	chr12:11188140-11341521	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1050050	chr12:11192046-11436359	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv1053783	chr12:11203509-11495584	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv1807067	chr12:11214215-11568895	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv1042134	chr12:11220712-11328131	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7970990	PRR4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11322200-11326000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:11322400-11325800	Active TSS	K562	blood
3	chr12:11322600-11325600	Active TSS	HSMMtube	muscle
4	chr12:11322800-11325200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:11322800-11325200	Active TSS	Stomach Smooth Muscle	stomach
6	chr12:11322800-11325400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr12:11322800-11325400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:11322800-11325400	Active TSS	A549	lung
9	chr12:11322800-11325600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:11322800-11325600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr12:11322800-11325800	Active TSS	GM12878-XiMat	blood
12	chr12:11322800-11326200	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr12:11323000-11325400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:11323000-11325400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:11323000-11325600	Active TSS	NHLF	lung
16	chr12:11323200-11325200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:11323200-11325200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr12:11323200-11325400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr12:11323200-11325400	Active TSS	Psoas Muscle	Psoas
20	chr12:11323200-11325400	Active TSS	Right Atrium	heart
21	chr12:11323200-11325400	Active TSS	HSMM	muscle
22	chr12:11323200-11325600	Active TSS	H1 Cell Line	embryonic stem cell
23	chr12:11323200-11325600	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr12:11323400-11325200	Active TSS	Primary T cells fromperipheralblood	blood
25	chr12:11323400-11325200	Active TSS	Aorta	Aorta
26	chr12:11323400-11325200	Active TSS	Colonic Mucosa	Colon
27	chr12:11323400-11325200	Active TSS	Fetal Muscle Trunk	muscle
28	chr12:11323400-11325200	Active TSS	Fetal Muscle Leg	muscle
29	chr12:11323400-11325200	Active TSS	Fetal Thymus	thymus
30	chr12:11323400-11325200	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr12:11323400-11325400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:11323400-11325400	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr12:11323400-11325400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:11323400-11325400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:11323400-11325400	Active TSS	Brain Anterior Caudate	brain
36	chr12:11323400-11325400	Active TSS	Fetal Intestine Large	intestine
37	chr12:11323400-11325400	Active TSS	Fetal Kidney	kidney
38	chr12:11323400-11325400	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr12:11323400-11325400	Active TSS	Fetal Stomach	stomach
40	chr12:11323400-11325400	Active TSS	HepG2	liver
41	chr12:11323400-11325400	Active TSS	NHDF-Ad	bronchial
42	chr12:11323400-11325400	Active TSS	NHEK	skin
43	chr12:11323400-11325600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:11323400-11325600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:11323400-11325600	Active TSS	Brain Germinal Matrix	brain
46	chr12:11323400-11325600	Active TSS	Fetal Intestine Small	intestine
47	chr12:11323400-11325800	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr12:11323400-11325800	Active TSS	HMEC	breast
49	chr12:11323400-11326000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:11323400-11326000	Active TSS	Muscle Satellite Cultured Cells	--

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