Variant report

Variant	rs12027630
Chromosome Location	chr1:94332917-94332918
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94332093..94333597-chr1:94363497..94365167,2	K562	blood:
2	chr1:94326500..94334861-chr1:94334949..94340833,11	K562	blood:
3	chr1:94329412..94331639-chr1:94331729..94334290,2	K562	blood:
4	chr1:94332079..94335914-chr1:94341026..94344306,4	K562	blood:
5	chr1:94330084..94333189-chr1:94373240..94377284,3	K562	blood:

Variant related genes	Relation type
ENSG00000067334	Chromatin interaction
ENSG00000023909	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10489602	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10489603	0.82[EUR][1000 genomes]
rs10489604	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782966	0.85[EUR][1000 genomes]
rs10782967	0.85[EUR][1000 genomes]
rs11165020	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165024	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12122113	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12134359	0.83[EUR][1000 genomes]
rs12137687	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12140446	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12143274	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12143279	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12563731	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12565614	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12566531	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12734571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739186	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12745990	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12752298	0.88[EUR][1000 genomes]
rs1884018	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143990	0.86[EUR][1000 genomes]
rs2235971	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2391322	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2747039	0.85[EUR][1000 genomes]
rs2747041	0.85[EUR][1000 genomes]
rs2747043	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2747045	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2747050	0.84[EUR][1000 genomes]
rs2818160	0.85[EUR][1000 genomes]
rs2818162	0.85[EUR][1000 genomes]
rs2818164	0.86[EUR][1000 genomes]
rs2818169	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3000471	0.86[EUR][1000 genomes]
rs3747965	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4075523	0.85[EUR][1000 genomes]
rs4141736	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4141737	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4240955	0.85[EUR][1000 genomes]
rs4240956	0.85[EUR][1000 genomes]
rs4314890	0.85[EUR][1000 genomes]
rs4847253	0.81[EUR][1000 genomes]
rs4847265	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6664719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685747	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7364910	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8179391	0.85[EUR][1000 genomes]
rs871854	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998755	chr1:94294015-94341712	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12027630	RP11-488P3.1	cis	Nerve Tibial	GTEx
rs12027630	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12027630	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs12027630	RP11-488P3.1	cis	lung	GTEx
rs12027630	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs12027630	RP11-488P3.1	cis	Artery Tibial	GTEx
rs12027630	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs12027630	RP11-488P3.1	cis	Thyroid	GTEx
rs12027630	RP11-488P3.1	cis	Stomach	GTEx
rs12027630	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94314200-94334200	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr1:94314200-94334400	Weak transcription	Brain Substantia Nigra	brain
3	chr1:94322200-94343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:94322600-94334200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:94328800-94334800	Weak transcription	Hela-S3	cervix
6	chr1:94329400-94334600	Weak transcription	A549	lung
7	chr1:94329600-94334000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:94329800-94333200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:94329800-94335200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:94329800-94343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:94330000-94333600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:94330000-94334200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:94330000-94334200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:94330000-94334600	Weak transcription	K562	blood
15	chr1:94330000-94337000	Weak transcription	Psoas Muscle	Psoas
16	chr1:94330000-94338800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:94330200-94334200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:94330200-94334600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:94330400-94334600	Weak transcription	HUVEC	blood vessel
20	chr1:94330600-94334200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:94330600-94334600	Weak transcription	HSMM	muscle
22	chr1:94330600-94335200	Weak transcription	NHLF	lung
23	chr1:94330600-94343600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:94330800-94334000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:94330800-94334600	Weak transcription	Fetal Brain Male	brain
26	chr1:94330800-94334600	Weak transcription	Osteobl	bone
27	chr1:94330800-94336800	Weak transcription	Spleen	Spleen
28	chr1:94331000-94333000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:94331000-94334000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:94331000-94334600	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:94331000-94339000	Weak transcription	Pancreas	Pancrea
32	chr1:94331200-94333200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:94331200-94334000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:94331200-94334200	Weak transcription	Adipose Nuclei	Adipose
35	chr1:94331200-94334200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:94331200-94334400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:94331400-94333000	Weak transcription	Fetal Brain Female	brain
38	chr1:94331400-94333200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:94331400-94334200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:94331400-94334200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:94331400-94334200	Weak transcription	Aorta	Aorta
42	chr1:94331400-94334200	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:94331400-94334200	Weak transcription	Placenta	Placenta
44	chr1:94331400-94334200	Weak transcription	Gastric	stomach
45	chr1:94331400-94334200	Weak transcription	HMEC	breast
46	chr1:94331400-94334400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:94331400-94334400	Weak transcription	NH-A	brain
48	chr1:94331400-94334600	Weak transcription	Fetal Intestine Large	intestine
49	chr1:94331400-94335200	Weak transcription	Colonic Mucosa	Colon
50	chr1:94331600-94333800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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