Variant report

Variant	rs1057285
Chromosome Location	chr1:175126845-175126846
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	chr1:175126264..175127026-chr1:175190372..175190985,2	MCF-7	breast:
2	chr1:175124723..175127210-chr1:175127837..175131491,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNN-1	chr1:175126670-175127199	ENSG00000227085

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10489327	0.84[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs10489328	0.83[MEX][hapmap]
rs12139941	0.84[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap]
rs16847872	0.84[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs2018318	0.83[MEX][hapmap]
rs2187958	0.89[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2269650	0.85[CHB][hapmap]
rs2269655	0.84[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs3737933	0.84[CHD][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.80[ASN][1000 genomes]
rs56237830	0.85[EUR][1000 genomes]
rs760486	0.81[CHB][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1057285	CACYBP	cis	parietal	SCAN
rs1057285	KIAA0040	cis	multi-tissue	Pritchard
rs1057285	KIAA0040	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175110200-175127400	Weak transcription	Left Ventricle	heart
2	chr1:175120000-175139400	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:175120200-175127600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:175121400-175127600	Weak transcription	Spleen	Spleen
5	chr1:175121600-175127200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:175121600-175128400	Weak transcription	Ovary	ovary
7	chr1:175121600-175130800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:175121800-175131200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:175122000-175128200	Weak transcription	Gastric	stomach
10	chr1:175122200-175132800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:175122200-175133400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:175122200-175136600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:175122400-175129400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:175122800-175127200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:175122800-175128200	Weak transcription	Aorta	Aorta
16	chr1:175123200-175127400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:175123200-175129600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:175123600-175127400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:175123800-175129400	Weak transcription	Fetal Intestine Small	intestine
20	chr1:175124000-175129000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:175124000-175140400	Weak transcription	Fetal Heart	heart
22	chr1:175124200-175129200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:175124400-175127400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:175124400-175128000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:175124400-175128200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:175124400-175128200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:175124400-175128400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:175124400-175128400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:175124400-175138200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:175124600-175127200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:175124600-175127200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:175124600-175128400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:175124600-175134600	Weak transcription	Small Intestine	intestine
34	chr1:175124800-175127600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:175124800-175128200	Weak transcription	Primary T cells from cord blood	blood
36	chr1:175124800-175128800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:175125000-175127000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:175125000-175127000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:175125000-175127000	Weak transcription	Thymus	Thymus
40	chr1:175125000-175127400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:175125000-175127400	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:175125000-175127600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:175125000-175127800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:175125000-175128200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:175125000-175128400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:175125000-175128800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:175125000-175128800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:175125000-175129000	Weak transcription	Fetal Intestine Large	intestine
49	chr1:175125000-175129200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:175125000-175132000	Weak transcription	Fetal Lung	lung

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