Variant report

Variant	rs12740875
Chromosome Location	chr1:151427666-151427667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151421812..151434588-chr1:151506621..151515599,30	MCF-7	breast:
2	chr1:151411841..151424302-chr1:151427210..151433048,24	MCF-7	breast:
3	chr1:151427202..151436068-chr1:151477865..151490153,60	MCF-7	breast:
4	chr1:151410628..151413374-chr1:151426124..151427883,2	MCF-7	breast:
5	chr1:151170967..151173717-chr1:151426450..151428273,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143442	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000238711	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000143367	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10736380	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749662	0.88[EUR][1000 genomes]
rs11204807	0.88[EUR][1000 genomes]
rs11204808	0.88[EUR][1000 genomes]
rs11204809	0.87[EUR][1000 genomes]
rs11204811	0.90[EUR][1000 genomes]
rs11204815	0.89[EUR][1000 genomes]
rs11204819	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204824	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11578888	0.90[EUR][1000 genomes]
rs11583968	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11584694	0.88[EUR][1000 genomes]
rs11589645	0.87[EUR][1000 genomes]
rs11801791	0.87[EUR][1000 genomes]
rs12025432	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12029691	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047617	0.88[EUR][1000 genomes]
rs12068166	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068368	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12071705	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120726	0.90[EUR][1000 genomes]
rs12125310	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12751531	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16833237	0.87[ASN][1000 genomes]
rs1887544	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1887545	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274533	0.88[EUR][1000 genomes]
rs2274534	0.87[EUR][1000 genomes]
rs2274535	0.88[EUR][1000 genomes]
rs2479379	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2479385	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2495380	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864122	0.88[EUR][1000 genomes]
rs3118720	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34884031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748550	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811409	0.81[ASN][1000 genomes]
rs3976737	0.86[EUR][1000 genomes]
rs4246526	0.90[EUR][1000 genomes]
rs4246527	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4364884	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4528122	0.90[EUR][1000 genomes]
rs4603	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4971042	0.88[EUR][1000 genomes]
rs4971043	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971049	0.87[EUR][1000 genomes]
rs61818037	0.85[EUR][1000 genomes]
rs61818039	0.88[EUR][1000 genomes]
rs6587572	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587573	0.88[EUR][1000 genomes]
rs6587577	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6587584	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587585	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6684333	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689436	0.88[EUR][1000 genomes]
rs7172	0.88[EUR][1000 genomes]
rs7542776	0.88[EUR][1000 genomes]
rs7546151	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7546933	0.88[EUR][1000 genomes]
rs9659456	0.88[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	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
2	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	esv1811070	chr1:151403570-151433317	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12740875	SELENBP1	cis	Thyroid	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151398400-151429600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:151401000-151430000	Weak transcription	Esophagus	oesophagus
3	chr1:151401600-151429200	Weak transcription	Spleen	Spleen
4	chr1:151405800-151428400	Weak transcription	Right Atrium	heart
5	chr1:151410200-151429800	Weak transcription	Lung	lung
6	chr1:151411400-151430000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:151412600-151429200	Weak transcription	Brain Germinal Matrix	brain
8	chr1:151413600-151429800	Weak transcription	Pancreas	Pancrea
9	chr1:151413600-151430000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:151413800-151428000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:151413800-151429400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:151413800-151429800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:151414000-151429600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:151414200-151430400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:151414400-151429000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:151414400-151429400	Weak transcription	Fetal Kidney	kidney
17	chr1:151414400-151429400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:151414600-151428200	Weak transcription	Fetal Brain Female	brain
19	chr1:151414600-151429000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:151414600-151429000	Weak transcription	Small Intestine	intestine
21	chr1:151414600-151429200	Weak transcription	Fetal Brain Male	brain
22	chr1:151414600-151430400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:151414800-151429600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:151415000-151429400	Weak transcription	Placenta	Placenta
25	chr1:151415200-151429000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr1:151416400-151429400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:151416800-151429600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:151417000-151428800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:151417000-151429200	Weak transcription	HUVEC	blood vessel
30	chr1:151417200-151428600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:151417200-151429000	Weak transcription	HSMMtube	muscle
32	chr1:151417400-151429600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:151417600-151428400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:151417600-151428400	Weak transcription	NHDF-Ad	bronchial
35	chr1:151417600-151428600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:151417600-151428800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:151417600-151428800	Weak transcription	Hela-S3	cervix
38	chr1:151417800-151428400	Weak transcription	Psoas Muscle	Psoas
39	chr1:151417800-151428600	Weak transcription	Stomach Mucosa	stomach
40	chr1:151418000-151429200	Weak transcription	Left Ventricle	heart
41	chr1:151418400-151428200	Weak transcription	Primary B cells from cord blood	blood
42	chr1:151418400-151428800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:151418400-151429400	Weak transcription	Brain Substantia Nigra	brain
44	chr1:151418400-151429400	Weak transcription	Fetal Heart	heart
45	chr1:151418400-151429600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:151418400-151429600	Weak transcription	Osteobl	bone
47	chr1:151418600-151429000	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:151418600-151429200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:151418600-151429200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:151418600-151429400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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