Variant report

Variant	rs1230666
Chromosome Location	chr1:114173410-114173411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11102638	1.00[LWK][hapmap]
rs12022213	1.00[LWK][hapmap]
rs12022849	1.00[LWK][hapmap]
rs12024139	1.00[LWK][hapmap]
rs12026682	1.00[LWK][hapmap]
rs12038473	1.00[LWK][hapmap]
rs12039944	1.00[LWK][hapmap]
rs1230661	0.84[MKK][hapmap]
rs1573996	1.00[LWK][hapmap]
rs17031716	0.84[MKK][hapmap]
rs1936927	1.00[LWK][hapmap]
rs6679677	1.00[ASW][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	nsv1012324	chr1:114135133-114206843	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv872161	chr1:114162194-114280135	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Thyroid peroxidase antibody levels	24586183	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1230666	PHTF1	cis	parietal	SCAN
rs1230666	CYB561D1	cis	parietal	SCAN
rs1230666	PHTF1	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114159000-114195000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:114159200-114194800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:114161600-114184600	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:114161600-114184600	Weak transcription	HepG2	liver
5	chr1:114161800-114199800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:114162200-114184600	Weak transcription	Left Ventricle	heart
7	chr1:114169200-114189400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:114169400-114184600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:114170800-114184600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:114171200-114174400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:114171600-114241400	Weak transcription	Right Ventricle	heart
12	chr1:114172000-114174400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:114172400-114173600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:114172400-114173600	Enhancers	Placenta	Placenta
15	chr1:114172400-114173800	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr1:114172400-114174000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:114172400-114182000	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:114172400-114184600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:114172400-114192600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:114172600-114173600	Strong transcription	Liver	Liver
21	chr1:114172600-114173600	Strong transcription	Pancreas	Pancrea
22	chr1:114172600-114173600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr1:114172600-114173600	Enhancers	HMEC	breast
24	chr1:114172600-114173800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:114172600-114173800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
26	chr1:114172600-114173800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:114172600-114173800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:114172600-114173800	ZNF genes & repeats	Lung	lung
29	chr1:114172600-114173800	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:114172800-114173800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:114172800-114173800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:114172800-114173800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:114172800-114173800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:114172800-114173800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:114172800-114173800	Strong transcription	Colonic Mucosa	Colon
36	chr1:114173000-114173600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr1:114173000-114173800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:114173000-114174000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:114173000-114174000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr1:114173000-114174000	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr1:114173000-114174000	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr1:114173000-114174000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:114173000-114174000	Strong transcription	Fetal Intestine Large	intestine
44	chr1:114173000-114174000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:114173000-114184600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:114173000-114184600	Weak transcription	Adipose Nuclei	Adipose
47	chr1:114173000-114214400	Weak transcription	Esophagus	oesophagus
48	chr1:114173000-114226800	Weak transcription	Aorta	Aorta
49	chr1:114173200-114173800	Strong transcription	Fetal Stomach	stomach
50	chr1:114173200-114174000	Enhancers	HUES48 Cell Line	embryonic stem cell

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