Variant report

Variant	rs843969
Chromosome Location	chr1:86102135-86102136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1047892	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1047895	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10782553	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10873709	0.81[ASN][1000 genomes]
rs10873710	0.81[ASN][1000 genomes]
rs1094359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161641	0.81[ASN][1000 genomes]
rs11161643	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11161645	0.92[ASN][1000 genomes]
rs11578464	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12128916	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1539444	0.81[EUR][1000 genomes]
rs1764285	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1764288	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1764289	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1764291	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1764292	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1764299	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1775988	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1775990	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1928626	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2389970	0.90[ASN][1000 genomes]
rs2785081	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2995537	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34448540	0.91[ASN][1000 genomes]
rs373787	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3753786	0.80[EUR][1000 genomes]
rs3767162	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs414618	0.81[ASN][1000 genomes]
rs418979	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs419409	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs424205	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs434853	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs447446	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4912441	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4949915	0.82[ASN][1000 genomes]
rs61783617	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6667094	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6689925	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6699497	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs709801	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520491	0.84[EUR][1000 genomes]
rs7532758	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs821379	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs821381	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs821386	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs821389	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs821391	0.86[AFR][1000 genomes]
rs821393	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs821394	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821395	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs821396	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821401	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9324154	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs952837	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9700177	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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	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	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1000290	chr1:86078495-86105379	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs843969	ZNHIT6	cis	lung	GTEx
rs843969	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs843969	ZNHIT6	cis	Esophagus Muscularis	GTEx
rs843969	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs843969	ZNHIT6	cis	Artery Aorta	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86083800-86103200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:86088400-86103000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:86088600-86103000	Weak transcription	NHEK	skin
4	chr1:86089400-86102600	Weak transcription	GM12878-XiMat	blood
5	chr1:86089400-86103000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:86091200-86103200	Weak transcription	Brain Angular Gyrus	brain
7	chr1:86091800-86102400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:86091800-86107600	Weak transcription	Colonic Mucosa	Colon
9	chr1:86093200-86102400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:86094000-86118600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:86094800-86103200	Weak transcription	Small Intestine	intestine
12	chr1:86095000-86102400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:86095000-86102800	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:86095000-86103200	Weak transcription	Fetal Heart	heart
15	chr1:86095200-86102400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:86095200-86102600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:86095200-86102800	Weak transcription	Fetal Stomach	stomach
18	chr1:86095200-86103000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:86095200-86103000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:86095200-86103000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:86095200-86103000	Weak transcription	Gastric	stomach
22	chr1:86095200-86103000	Weak transcription	Ovary	ovary
23	chr1:86095200-86103000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:86095200-86103000	Weak transcription	Spleen	Spleen
25	chr1:86095200-86104200	Weak transcription	Psoas Muscle	Psoas
26	chr1:86095200-86104400	Weak transcription	Right Ventricle	heart
27	chr1:86095400-86102600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:86095400-86102800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:86095400-86103000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:86095400-86103000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:86095400-86103000	Weak transcription	Brain Anterior Caudate	brain
32	chr1:86095400-86103000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:86095400-86107600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:86095400-86119000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:86095400-86134800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:86095600-86103000	Weak transcription	Fetal Lung	lung
37	chr1:86095600-86103800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:86095600-86104000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:86095600-86104000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:86095600-86117000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:86095800-86102600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:86095800-86103000	Weak transcription	HSMMtube	muscle
43	chr1:86095800-86103200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:86096000-86102400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:86096000-86103000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:86096000-86104000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:86096200-86102600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:86096200-86102800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:86096200-86103400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:86096200-86103800	Weak transcription	HepG2	liver

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