Variant report

Variant	rs821391
Chromosome Location	chr1:86114132-86114133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1047895	0.82[AFR][1000 genomes]
rs1094359	0.86[AFR][1000 genomes]
rs1764285	0.80[EUR][1000 genomes]
rs1764288	0.83[AFR][1000 genomes]
rs1764299	0.91[AFR][1000 genomes]
rs2995537	0.88[AFR][1000 genomes]
rs3767162	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs61783617	0.83[AFR][1000 genomes]
rs6689925	0.88[AFR][1000 genomes]
rs6699497	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs709801	0.89[AFR][1000 genomes]
rs821379	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs821381	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs821386	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs821389	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs821393	0.82[AFR][1000 genomes]
rs821394	0.89[AFR][1000 genomes]
rs821396	0.88[AFR][1000 genomes]
rs821401	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs843969	0.86[AFR][1000 genomes]
rs9324154	0.87[AFR][1000 genomes]
rs952837	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9700177	0.88[AFR][1000 genomes];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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs821391	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs821391	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs821391	ZNHIT6	cis	Artery Aorta	GTEx
rs821391	ZNHIT6	cis	lung	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86094000-86118600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:86095400-86119000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:86095400-86134800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:86095600-86117000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:86096200-86115600	Weak transcription	NH-A	brain
6	chr1:86102800-86118200	Weak transcription	K562	blood
7	chr1:86103400-86116000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:86103400-86173000	Weak transcription	Pancreas	Pancrea
9	chr1:86103600-86115000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:86103600-86116400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:86103600-86117800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:86103600-86119000	Weak transcription	Spleen	Spleen
13	chr1:86103600-86119400	Weak transcription	Fetal Heart	heart
14	chr1:86103600-86119800	Weak transcription	NHLF	lung
15	chr1:86103600-86120200	Weak transcription	HMEC	breast
16	chr1:86103600-86141200	Weak transcription	Thymus	Thymus
17	chr1:86103600-86142200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:86103600-86145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:86103600-86145600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:86103600-86157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:86103600-86172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:86103600-86172600	Weak transcription	Gastric	stomach
23	chr1:86104400-86116000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:86104400-86116000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:86104600-86115000	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:86104600-86117800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:86105000-86118000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:86105200-86114400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:86105200-86114600	Weak transcription	Psoas Muscle	Psoas
30	chr1:86105200-86115200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:86105200-86118000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:86105200-86118800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:86105200-86119000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:86106000-86141200	Weak transcription	Lung	lung
35	chr1:86108000-86118800	Weak transcription	Colonic Mucosa	Colon
36	chr1:86108400-86114800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:86111000-86114800	Weak transcription	Primary T cells from cord blood	blood
38	chr1:86113000-86119000	Weak transcription	Fetal Brain Male	brain
39	chr1:86113200-86114200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:86113200-86118400	Weak transcription	Hela-S3	cervix
41	chr1:86113200-86119000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:86113600-86116400	Strong transcription	HSMM	muscle
43	chr1:86113800-86114200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
44	chr1:86113800-86114200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:86113800-86114200	ZNF genes & repeats	Adipose Nuclei	Adipose
46	chr1:86113800-86114200	ZNF genes & repeats	Fetal Lung	lung
47	chr1:86113800-86114200	ZNF genes & repeats	Osteobl	bone
48	chr1:86113800-86114400	ZNF genes & repeats	Fetal Thymus	thymus
49	chr1:86113800-86115000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
50	chr1:86113800-86115000	ZNF genes & repeats	GM12878-XiMat	blood

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