Variant report

Variant	rs16934061
Chromosome Location	chr12:29395195-29395196
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29394990..29395795-chr12:29470382..29471222,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257176	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11608616	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11609540	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11610910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11611687	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11612172	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11613628	0.84[EUR][1000 genomes]
rs11614129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615636	0.91[EUR][1000 genomes]
rs12809077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12810064	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12810315	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12813996	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12814180	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12814930	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12815222	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12816511	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12817163	0.90[EUR][1000 genomes]
rs12817825	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12817985	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12821498	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12822770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12823372	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12823422	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12823485	0.84[EUR][1000 genomes]
rs12823903	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12826064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12829666	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12830274	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12830493	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12830906	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12832263	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1988943	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2350312	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2882377	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34162895	0.80[AMR][1000 genomes]
rs35618989	0.81[AMR][1000 genomes]
rs35636563	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36040692	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36126531	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4369447	0.99[EUR][1000 genomes]
rs67280216	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67324531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7134744	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7299158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7299635	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7299663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314594	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7961336	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7964254	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7979654	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16934061	RP11-996F15.2	cis	Artery Tibial	GTEx
rs16934061	RP11-996F15.2	cis	lung	GTEx
rs16934061	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs16934061	RP11-996F15.2	cis	Thyroid	GTEx
rs16934061	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs16934061	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs16934061	RP11-996F15.2	cis	Nerve Tibial	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29391600-29400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:29391800-29400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:29392400-29395400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:29392800-29396000	Enhancers	Placenta	Placenta
5	chr12:29393200-29396000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr12:29393200-29397000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr12:29393400-29395400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:29393400-29395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:29393400-29396000	Enhancers	Duodenum Mucosa	Duodenum
10	chr12:29393400-29396600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:29394000-29395800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr12:29394000-29395800	Enhancers	Stomach Smooth Muscle	stomach
13	chr12:29394000-29396200	Enhancers	Colonic Mucosa	Colon
14	chr12:29394000-29396200	Enhancers	NHDF-Ad	bronchial
15	chr12:29394200-29395400	Enhancers	Primary B cells from cord blood	blood
16	chr12:29394200-29396000	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr12:29394200-29396200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr12:29394200-29396200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr12:29394200-29396800	Enhancers	Stomach Mucosa	stomach
20	chr12:29394400-29395800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:29394400-29395800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:29394400-29396000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:29394400-29396200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr12:29394400-29396400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:29394400-29397600	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr12:29394400-29397800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:29394600-29395200	Enhancers	Fetal Stomach	stomach
28	chr12:29394600-29395200	Enhancers	Fetal Thymus	thymus
29	chr12:29394600-29395200	Enhancers	HSMMtube	muscle
30	chr12:29394600-29395400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr12:29394600-29395600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr12:29394600-29395600	Enhancers	H9 Cell Line	embryonic stem cell
33	chr12:29394600-29395600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:29394600-29395600	Enhancers	Brain Substantia Nigra	brain
35	chr12:29394600-29395600	Enhancers	Right Atrium	heart
36	chr12:29394600-29395600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr12:29394600-29395600	Enhancers	HSMM	muscle
38	chr12:29394600-29395800	Enhancers	Brain Angular Gyrus	brain
39	chr12:29394600-29395800	Enhancers	Fetal Muscle Leg	muscle
40	chr12:29394600-29395800	Enhancers	Hela-S3	cervix
41	chr12:29394600-29395800	Enhancers	NHLF	lung
42	chr12:29394600-29396000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr12:29394600-29396200	Enhancers	H1 Cell Line	embryonic stem cell
44	chr12:29394600-29396200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:29394600-29396200	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr12:29394600-29396200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:29394600-29396200	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr12:29394600-29396200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:29394600-29396200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr12:29394600-29396200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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