Variant report

Variant	rs61928646
Chromosome Location	chr12:11327314-11327315
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	POLR2A	chr12:11327147-11327697	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:11327097-11327357	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:11325711..11328028-chr12:11332674..11335077,2	K562	blood:
2	chr12:11321748..11327565-chr12:11327784..11333912,14	MCF-7	breast:
3	chr12:11326790..11329345-chr12:11330898..11332446,2	K562	blood:
4	chr12:11326790..11329345-chr12:11330898..11332485,3	K562	blood:

Variant related genes	Relation type
TAS2R14	TF binding region
PRR4	TF binding region
ENSG00000256712	TF binding region
ENSG00000256629	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11557132	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1451765	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1451772	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1551191	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1650020	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1650029	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1650030	0.87[ASN][1000 genomes]
rs1650031	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1650053	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1669410	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1669412	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1669414	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1669418	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1669422	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1817104	0.87[ASN][1000 genomes]
rs2123006	0.87[ASN][1000 genomes]
rs2123007	0.87[ASN][1000 genomes]
rs2167481	0.87[ASN][1000 genomes]
rs2416544	0.87[ASN][1000 genomes]
rs2416545	0.87[ASN][1000 genomes]
rs2416546	0.87[ASN][1000 genomes]
rs2416547	0.87[ASN][1000 genomes]
rs2559581	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2600355	0.83[ASN][1000 genomes]
rs2708331	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319267	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319268	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319271	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319272	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs319273	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs319274	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34018339	0.87[ASN][1000 genomes]
rs34270405	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34531956	0.87[ASN][1000 genomes]
rs34590962	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35119575	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35151793	0.87[ASN][1000 genomes]
rs35183723	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3911800	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4763638	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61928618	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61928619	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61928642	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61928643	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61928644	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6488347	0.80[ASN][1000 genomes]
rs6488348	0.80[ASN][1000 genomes]
rs6488349	0.80[ASN][1000 genomes]
rs6488350	0.80[ASN][1000 genomes]
rs7969625	0.87[ASN][1000 genomes]
rs8300	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs61928646	PRR4	cis	Muscle Skeletal	GTEx
rs61928646	PRR4	cis	lung	GTEx
rs61928646	PRR4	cis	Nerve Tibial	GTEx
rs61928646	RP11-434C1.1	cis	Nerve Tibial	GTEx
rs61928646	RP11-434C1.1	cis	lung	GTEx
rs61928646	TAS2R14	cis	Esophagus Muscularis	GTEx
rs61928646	PRR4	cis	Thyroid	GTEx
rs61928646	RP11-434C1.1	cis	Heart Left Ventricle	GTEx
rs61928646	PRR4	cis	Whole Blood	GTEx
rs61928646	PRR4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11325000-11335600	Weak transcription	Left Ventricle	heart
2	chr12:11325200-11327800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:11325200-11328400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:11325200-11328600	Weak transcription	Thymus	Thymus
5	chr12:11325200-11330000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr12:11325200-11330400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr12:11325200-11332200	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:11325200-11332200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:11325400-11331400	Weak transcription	Psoas Muscle	Psoas
10	chr12:11325400-11331800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:11325400-11332000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:11325600-11327600	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr12:11325600-11328800	Weak transcription	Fetal Intestine Large	intestine
14	chr12:11325600-11329000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr12:11325600-11330000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:11325600-11331400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:11325600-11332200	Weak transcription	Brain Germinal Matrix	brain
18	chr12:11325600-11334400	Weak transcription	Primary B cells from cord blood	blood
19	chr12:11325600-11338200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr12:11325800-11328000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:11325800-11329000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:11325800-11329600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:11326000-11328000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr12:11326000-11328400	Weak transcription	Hela-S3	cervix
25	chr12:11326000-11328800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:11326000-11329000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:11326000-11330000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:11326000-11330400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:11326000-11330400	Weak transcription	Fetal Lung	lung
30	chr12:11326000-11330800	Weak transcription	HUVEC	blood vessel
31	chr12:11326000-11331000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:11326000-11331800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:11326000-11334400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:11326200-11327800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:11326200-11328000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:11326200-11328800	Weak transcription	Ovary	ovary
37	chr12:11326200-11329200	Weak transcription	Fetal Brain Female	brain
38	chr12:11326200-11331400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:11326200-11331400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:11326200-11331600	Weak transcription	HMEC	breast
41	chr12:11326200-11331800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:11326200-11334600	Weak transcription	Liver	Liver
43	chr12:11326200-11338600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:11326400-11327400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:11326400-11328000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:11326400-11328200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:11326400-11328800	Weak transcription	GM12878-XiMat	blood
48	chr12:11326400-11329000	Weak transcription	Fetal Kidney	kidney
49	chr12:11326400-11329800	Weak transcription	A549	lung
50	chr12:11326400-11330000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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