Variant report

Variant	rs12139941
Chromosome Location	chr1:175127616-175127617
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	chr1:174991534..174994499-chr1:175127289..175129850,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNN-1	chr1:175127396-175127666	ENSG00000227085

Variant related genes	Relation type
ENSG00000206659	Chromatin interaction
ENSG00000120333	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10489327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489328	0.82[MEX][hapmap]
rs1057285	0.84[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap]
rs11809587	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135071	1.00[AFR][1000 genomes]
rs12139918	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018318	0.82[MEX][hapmap]
rs2187958	0.91[MEX][hapmap]
rs2269655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737933	0.88[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.80[ASN][1000 genomes]
rs56237830	1.00[AFR][1000 genomes]
rs60259517	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522101	chr1:175109517-175151183	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv429924	chr1:175110480-175134314	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12139941	CACYBP	cis	cerebellum	SCAN
rs12139941	CACYBP	cis	parietal	SCAN
rs12139941	MRPS14	cis	cerebellum	SCAN
rs12139941	KIAA0040	Cis_1M	lymphoblastoid	RTeQTL
rs12139941	C1orf112	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175120000-175139400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:175121600-175128400	Weak transcription	Ovary	ovary
3	chr1:175121600-175130800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:175121800-175131200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:175122000-175128200	Weak transcription	Gastric	stomach
6	chr1:175122200-175132800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:175122200-175133400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:175122200-175136600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:175122400-175129400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:175122800-175128200	Weak transcription	Aorta	Aorta
11	chr1:175123200-175129600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:175123800-175129400	Weak transcription	Fetal Intestine Small	intestine
13	chr1:175124000-175129000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:175124000-175140400	Weak transcription	Fetal Heart	heart
15	chr1:175124200-175129200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:175124400-175128000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:175124400-175128200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:175124400-175128200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:175124400-175128400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:175124400-175128400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:175124400-175138200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:175124600-175128400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:175124600-175134600	Weak transcription	Small Intestine	intestine
24	chr1:175124800-175128200	Weak transcription	Primary T cells from cord blood	blood
25	chr1:175124800-175128800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:175125000-175127800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:175125000-175128200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:175125000-175128400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:175125000-175128800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:175125000-175128800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:175125000-175129000	Weak transcription	Fetal Intestine Large	intestine
32	chr1:175125000-175129200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:175125000-175132000	Weak transcription	Fetal Lung	lung
34	chr1:175125200-175127800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:175125200-175127800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:175125200-175128400	Weak transcription	GM12878-XiMat	blood
37	chr1:175125200-175128600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:175125400-175128400	Weak transcription	Right Ventricle	heart
39	chr1:175125400-175132400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:175125600-175129400	Weak transcription	Fetal Kidney	kidney
41	chr1:175125800-175128800	Weak transcription	Fetal Stomach	stomach
42	chr1:175126200-175129400	Weak transcription	Esophagus	oesophagus
43	chr1:175126400-175128200	Enhancers	HMEC	breast
44	chr1:175126600-175128600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:175126800-175127800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:175126800-175129000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:175126800-175129400	Weak transcription	Psoas Muscle	Psoas
48	chr1:175126800-175138200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:175126800-175141800	Strong transcription	Primary B cells from cord blood	blood
50	chr1:175126800-175148800	Strong transcription	Primary monocytes fromperipheralblood	blood

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