Variant report

Variant	rs233055
Chromosome Location	chr1:85798486-85798487
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1001604	0.83[EUR][1000 genomes]
rs10489513	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161607	0.80[EUR][1000 genomes]
rs1146379	0.92[ASN][1000 genomes]
rs12044537	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12047422	0.80[EUR][1000 genomes]
rs12124170	0.87[EUR][1000 genomes]
rs1498373	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1498375	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs173026	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs18582	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1884139	0.80[EUR][1000 genomes]
rs2011825	0.80[EUR][1000 genomes]
rs2012683	0.82[EUR][1000 genomes]
rs2207368	0.81[EUR][1000 genomes]
rs2268667	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2300634	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2300637	0.87[EUR][1000 genomes]
rs233047	0.87[EUR][1000 genomes]
rs233050	0.81[EUR][1000 genomes]
rs233053	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233054	0.81[EUR][1000 genomes]
rs233057	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233058	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233059	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233060	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233061	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233062	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233066	0.87[EUR][1000 genomes]
rs233067	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs233068	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs233069	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs233071	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs233072	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233074	0.82[EUR][1000 genomes]
rs233091	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs233093	0.87[EUR][1000 genomes]
rs233095	0.87[EUR][1000 genomes]
rs233097	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs233099	0.87[EUR][1000 genomes]
rs233108	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233109	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs233112	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs233113	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233114	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233115	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233118	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs233119	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233120	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs233121	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233124	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233127	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233130	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233131	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233132	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233133	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087894	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3768227	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs423105	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4949890	0.86[EUR][1000 genomes]
rs506082	0.91[ASN][1000 genomes]
rs6576763	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6576765	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6576766	0.88[ASN][1000 genomes]
rs66811655	0.88[EUR][1000 genomes]
rs6704103	0.80[EUR][1000 genomes]
rs67611930	0.81[EUR][1000 genomes]
rs72724606	0.80[EUR][1000 genomes]
rs761601	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs997251	0.81[EUR][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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs233055	ZNHIT6	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85790600-85800000	Enhancers	HUVEC	blood vessel
2	chr1:85792200-85806000	Weak transcription	Fetal Kidney	kidney
3	chr1:85793200-85798600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:85795200-85798600	Weak transcription	Fetal Intestine Large	intestine
5	chr1:85796200-85799800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:85796600-85798600	Enhancers	HSMMtube	muscle
7	chr1:85796600-85799600	Enhancers	Osteobl	bone
8	chr1:85796600-85801800	Weak transcription	Gastric	stomach
9	chr1:85796600-85804000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:85796600-85809400	Weak transcription	Stomach Mucosa	stomach
11	chr1:85796800-85798600	Weak transcription	Ovary	ovary
12	chr1:85796800-85798600	Enhancers	NHDF-Ad	bronchial
13	chr1:85796800-85799600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:85796800-85804200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:85796800-85805400	Weak transcription	Aorta	Aorta
16	chr1:85796800-85805400	Weak transcription	HepG2	liver
17	chr1:85796800-85806400	Weak transcription	Small Intestine	intestine
18	chr1:85796800-85809600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:85797000-85800600	Weak transcription	HMEC	breast
20	chr1:85797000-85805000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:85797400-85798800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:85797400-85799000	Enhancers	Fetal Muscle Trunk	muscle
23	chr1:85797400-85800200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:85797600-85798800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr1:85797600-85799200	Genic enhancers	HSMM	muscle
26	chr1:85797600-85800400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:85797600-85803600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:85797800-85798600	Enhancers	Pancreas	Pancrea
29	chr1:85797800-85798800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:85797800-85799200	Strong transcription	Fetal Intestine Small	intestine
31	chr1:85798000-85798800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:85798000-85798800	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr1:85798000-85799000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:85798000-85799200	Genic enhancers	Muscle Satellite Cultured Cells	--
35	chr1:85798200-85798600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:85798200-85798600	ZNF genes & repeats	Spleen	Spleen
37	chr1:85798200-85798800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:85798200-85798800	ZNF genes & repeats	Lung	lung
39	chr1:85798200-85799000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:85798200-85799000	ZNF genes & repeats	Fetal Stomach	stomach
41	chr1:85798200-85799600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:85798200-85800400	Weak transcription	NH-A	brain
43	chr1:85798400-85798600	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr1:85798400-85798600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr1:85798400-85798800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:85798400-85798800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr1:85798400-85798800	Enhancers	Fetal Muscle Leg	muscle
48	chr1:85798400-85803400	Weak transcription	Hela-S3	cervix
49	chr1:85798400-85804200	Weak transcription	Right Ventricle	heart
50	chr1:85798400-85806200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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