Variant report

Variant	rs12039334
Chromosome Location	chr1:151049918-151049919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151041720..151043462-chr1:151048859..151051692,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197622	Chromatin interaction
ENSG00000143458	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10788798	0.89[EUR][1000 genomes]
rs10788799	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11204777	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11204778	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11204780	0.87[EUR][1000 genomes]
rs12039522	0.81[ASN][1000 genomes]
rs12039542	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12040729	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12049116	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12117163	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1524773	0.85[EUR][1000 genomes]
rs2140709	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3738481	0.86[EUR][1000 genomes]
rs3806386	0.82[EUR][1000 genomes]
rs3806387	0.82[EUR][1000 genomes]
rs4970939	0.88[EUR][1000 genomes]
rs4970993	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4970998	0.82[EUR][1000 genomes]
rs4970999	0.84[EUR][1000 genomes]
rs61819199	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6587553	0.80[EUR][1000 genomes]
rs6668894	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12039334	BNIPL	cis	lung	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151043600-151050200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:151043800-151056200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:151044000-151062800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:151044000-151066800	Weak transcription	Ovary	ovary
5	chr1:151044000-151079600	Weak transcription	Spleen	Spleen
6	chr1:151044000-151080600	Weak transcription	Esophagus	oesophagus
7	chr1:151044200-151069800	Weak transcription	HSMM	muscle
8	chr1:151044200-151070800	Weak transcription	Fetal Lung	lung
9	chr1:151044200-151080200	Weak transcription	Aorta	Aorta
10	chr1:151044400-151061600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:151044400-151062200	Weak transcription	Liver	Liver
12	chr1:151044400-151079000	Weak transcription	Left Ventricle	heart
13	chr1:151044400-151079600	Weak transcription	Lung	lung
14	chr1:151044400-151090200	Weak transcription	Gastric	stomach
15	chr1:151044400-151090400	Weak transcription	Right Ventricle	heart
16	chr1:151044400-151103600	Weak transcription	Small Intestine	intestine
17	chr1:151044600-151052000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:151044600-151052000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:151044600-151054200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:151044600-151061200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:151044600-151069600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:151044600-151069800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:151044600-151069800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:151044600-151070000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:151044600-151076000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:151044600-151080400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:151044600-151080600	Weak transcription	Brain Anterior Caudate	brain
28	chr1:151044600-151081000	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:151044800-151061400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:151044800-151062800	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:151044800-151065400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:151044800-151066200	Weak transcription	Brain Substantia Nigra	brain
33	chr1:151044800-151069800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:151044800-151070400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:151044800-151079600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:151044800-151080200	Weak transcription	Fetal Brain Female	brain
37	chr1:151044800-151089400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:151044800-151098800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:151045000-151051200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:151045000-151051400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:151045000-151054600	Weak transcription	Psoas Muscle	Psoas
42	chr1:151045000-151062800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:151045000-151065400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:151045000-151065400	Weak transcription	Adipose Nuclei	Adipose
45	chr1:151045000-151070400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:151045000-151079400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:151045000-151080000	Weak transcription	Brain Angular Gyrus	brain
48	chr1:151045000-151080400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:151045200-151081000	Weak transcription	Placenta	Placenta
50	chr1:151045800-151062800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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