Variant report

Variant	rs1259291
Chromosome Location	chr3:120135534-120135535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120066683..120069850-chr3:120134285..120137656,5	MCF-7	breast:
2	chr3:120066496..120069971-chr3:120134010..120137845,6	MCF-7	breast:
3	chr3:120133952..120135964-chr3:121186805..121189623,2	MCF-7	breast:
4	chr3:119961477..119964195-chr3:120134350..120136316,3	MCF-7	breast:
5	chr3:119962768..119964437-chr3:120135476..120136895,30	MCF-7	breast:
6	chr3:120135445..120137288-chr3:120277206..120278376,12	MCF-7	breast:
7	chr3:119961796..119964047-chr3:120135091..120137242,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175697	Chromatin interaction
ENSG00000163428	Chromatin interaction
ENSG00000240661	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1147702	0.92[ASN][1000 genomes]
rs1147704	0.82[ASN][1000 genomes]
rs1147705	0.96[ASN][1000 genomes]
rs1259292	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259293	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1259294	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259295	0.88[ASN][1000 genomes]
rs1259296	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259297	0.89[ASN][1000 genomes]
rs1259307	0.86[ASN][1000 genomes]
rs1259327	0.86[ASN][1000 genomes]
rs1356112	0.84[AMR][1000 genomes]
rs1617553	0.81[AMR][1000 genomes]
rs1716839	0.81[AMR][1000 genomes]
rs1733324	0.81[AMR][1000 genomes]
rs2673701	0.81[AMR][1000 genomes]
rs2673704	0.89[ASN][1000 genomes]
rs2700260	0.87[ASN][1000 genomes]
rs2700261	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs916510	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs916511	0.88[ASN][1000 genomes]
rs916512	0.82[ASN][1000 genomes]
rs939500	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1259291	GPR156	cis	Esophagus Muscularis	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120114400-120143200	Weak transcription	Small Intestine	intestine
2	chr3:120115800-120151000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:120118800-120135600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:120122200-120136000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:120122400-120135800	Weak transcription	A549	lung
6	chr3:120127400-120135600	Weak transcription	Fetal Thymus	thymus
7	chr3:120128200-120137600	Weak transcription	Gastric	stomach
8	chr3:120128400-120135600	Weak transcription	Brain Germinal Matrix	brain
9	chr3:120128400-120135600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:120128400-120136200	Weak transcription	Fetal Brain Female	brain
11	chr3:120128600-120135600	Weak transcription	Esophagus	oesophagus
12	chr3:120128600-120135600	Weak transcription	Pancreas	Pancrea
13	chr3:120128600-120135600	Weak transcription	Spleen	Spleen
14	chr3:120128800-120135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:120129800-120135600	Weak transcription	HMEC	breast
16	chr3:120130600-120135800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:120131000-120135600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:120131000-120135600	Weak transcription	Colonic Mucosa	Colon
19	chr3:120131200-120135600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:120131200-120135600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:120131200-120135800	Weak transcription	Ovary	ovary
22	chr3:120131200-120136000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:120131400-120135600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:120131400-120135600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:120131600-120135600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:120132400-120135600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:120132400-120135600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:120132400-120135600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:120132400-120135600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:120132400-120135600	Weak transcription	Fetal Intestine Small	intestine
31	chr3:120132400-120135800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr3:120132400-120135800	Weak transcription	Stomach Mucosa	stomach
33	chr3:120132400-120135800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:120132400-120136600	Weak transcription	Aorta	Aorta
35	chr3:120132600-120135600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:120132600-120135600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:120132600-120135600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:120132600-120135600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:120132600-120135600	Weak transcription	Fetal Brain Male	brain
40	chr3:120132600-120135600	Weak transcription	Fetal Kidney	kidney
41	chr3:120132600-120135600	Weak transcription	Placenta	Placenta
42	chr3:120132600-120135600	Weak transcription	NHEK	skin
43	chr3:120132600-120135800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:120132600-120136400	Weak transcription	HSMMtube	muscle
45	chr3:120132800-120135600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:120133200-120136000	Weak transcription	Fetal Intestine Large	intestine
47	chr3:120133800-120135600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:120134000-120135600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:120134000-120135600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr3:120134000-120135600	Strong transcription	Placenta Amnion	Placenta Amnion

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