Variant report

Variant	rs7313179
Chromosome Location	chr12:124009190-124009191
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124003058..124006753-chr12:124009013..124012498,5	MCF-7	breast:
2	chr12:123991512..123994441-chr12:124007477..124009377,2	MCF-7	breast:
3	chr12:124008463..124013124-chr12:124014349..124019990,8	MCF-7	breast:
4	chr12:124002890..124005569-chr12:124009063..124010830,3	MCF-7	breast:
5	chr12:124007811..124010230-chr12:124011879..124014265,2	MCF-7	breast:
6	chr12:124008800..124013373-chr12:124015066..124019267,4	K562	blood:

Variant related genes	Relation type
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1057879	0.87[ASN][1000 genomes]
rs10846526	0.84[ASN][1000 genomes]
rs2048615	0.87[ASN][1000 genomes]
rs2333831	0.87[ASN][1000 genomes]
rs28371124	0.87[ASN][1000 genomes]
rs28403439	0.93[ASN][1000 genomes]
rs28430750	0.87[ASN][1000 genomes]
rs28454032	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28465339	0.84[ASN][1000 genomes]
rs28478446	0.87[ASN][1000 genomes]
rs28497190	0.87[ASN][1000 genomes]
rs28535724	0.93[ASN][1000 genomes]
rs28539789	0.84[ASN][1000 genomes]
rs28580741	0.82[ASN][1000 genomes]
rs28654896	0.84[ASN][1000 genomes]
rs28673982	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28701527	0.87[ASN][1000 genomes]
rs28707421	0.87[ASN][1000 genomes]
rs28711456	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28712858	0.87[ASN][1000 genomes]
rs28741988	0.87[ASN][1000 genomes]
rs28758342	0.84[ASN][1000 genomes]
rs4930716	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5027860	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61953537	0.82[ASN][1000 genomes]
rs61953538	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61953539	0.93[ASN][1000 genomes]
rs61953543	0.93[ASN][1000 genomes]
rs61953552	0.84[ASN][1000 genomes]
rs61953557	0.84[ASN][1000 genomes]
rs7307227	0.84[ASN][1000 genomes]
rs7965334	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9697543	0.84[ASN][1000 genomes]
rs9697721	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription 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	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7313179	RP11-486O12.2	cis	Muscle Skeletal	GTEx
rs7313179	RP11-486O12.2	cis	Thyroid	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123944600-124012200	Strong transcription	Fetal Stomach	stomach
2	chr12:123970000-124016400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr12:123992600-124012800	Weak transcription	Thymus	Thymus
4	chr12:123993600-124011200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:123994400-124016200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:123994600-124016200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:123995200-124016400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:123995400-124009400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:123999200-124015800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr12:123999400-124016400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:124000200-124012400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:124000600-124009200	Strong transcription	Liver	Liver
13	chr12:124000600-124009200	Strong transcription	Fetal Brain Female	brain
14	chr12:124000600-124009200	Strong transcription	Ovary	ovary
15	chr12:124000600-124009200	Strong transcription	Spleen	Spleen
16	chr12:124000600-124009400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:124000600-124009400	Strong transcription	Adipose Nuclei	Adipose
18	chr12:124000600-124009600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:124000600-124009800	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:124000600-124011400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:124000600-124015000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr12:124001000-124016400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:124001200-124017400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:124001400-124017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:124002000-124016800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:124003000-124015400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:124004000-124009200	Strong transcription	Fetal Intestine Large	intestine
28	chr12:124004000-124009200	Strong transcription	Lung	lung
29	chr12:124004200-124009200	Strong transcription	Fetal Lung	lung
30	chr12:124004600-124009200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:124004600-124009200	Strong transcription	Brain Cingulate Gyrus	brain
32	chr12:124004600-124009200	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr12:124004600-124011200	Weak transcription	Psoas Muscle	Psoas
34	chr12:124004600-124016800	Weak transcription	Stomach Mucosa	stomach
35	chr12:124004800-124009200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:124004800-124009200	Strong transcription	Brain Angular Gyrus	brain
37	chr12:124004800-124009200	Strong transcription	Osteobl	bone
38	chr12:124004800-124009400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:124004800-124009400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:124004800-124009400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:124004800-124009400	Strong transcription	Brain Anterior Caudate	brain
42	chr12:124004800-124009400	Strong transcription	Colon Smooth Muscle	Colon
43	chr12:124004800-124009400	Strong transcription	A549	lung
44	chr12:124004800-124009400	Strong transcription	HepG2	liver
45	chr12:124004800-124014600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr12:124004800-124016600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr12:124005000-124009200	Strong transcription	Brain Hippocampus Middle	brain
48	chr12:124005000-124009200	Strong transcription	HMEC	breast
49	chr12:124005000-124009200	Strong transcription	HSMMtube	muscle
50	chr12:124005200-124009200	Strong transcription	Stomach Smooth Muscle	stomach

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