Variant report

Variant	rs9847585
Chromosome Location	chr3:49414062-49414063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1009051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs10154992	1.00[CEU][hapmap]
rs10155014	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10865956	1.00[CEU][hapmap]
rs11130183	1.00[CEU][hapmap]
rs11130186	0.91[CEU][hapmap]
rs11130190	0.83[EUR][1000 genomes]
rs11719762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11720657	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs11928090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs12583	1.00[CEU][hapmap]
rs13096474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs13322887	1.00[CEU][hapmap]
rs1464569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs17080510	1.00[CHB][hapmap]
rs1982861	1.00[CEU][hapmap]
rs2140270	1.00[CEU][hapmap]
rs2177268	1.00[CEU][hapmap]
rs2312462	1.00[CEU][hapmap]
rs3448	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3866330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs3870339	0.95[CEU][hapmap]
rs3905330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4241407	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4955413	0.86[EUR][1000 genomes]
rs4955417	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4955430	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4955439	1.00[CEU][hapmap]
rs4955443	1.00[CEU][hapmap]
rs62259943	0.81[EUR][1000 genomes]
rs6446256	1.00[CEU][hapmap]
rs6446257	1.00[CEU][hapmap]
rs6446262	0.85[EUR][1000 genomes]
rs6769744	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6769821	1.00[CEU][hapmap]
rs6775069	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6778080	1.00[CEU][hapmap]
rs6783003	1.00[CEU][hapmap]
rs6796147	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6805609	1.00[CEU][hapmap]
rs6809851	1.00[CEU][hapmap]
rs7429661	1.00[CEU][hapmap]
rs7619016	1.00[CEU][hapmap]
rs7626076	1.00[CEU][hapmap]
rs7644148	1.00[CEU][hapmap]
rs7647973	1.00[CEU][hapmap]
rs7653505	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs8897	1.00[CEU][hapmap]
rs940045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs974495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9757181	1.00[CEU][hapmap]
rs9812360	0.82[EUR][1000 genomes]
rs9834003	1.00[CEU][hapmap]
rs9842132	0.81[EUR][1000 genomes]
rs9860055	1.00[CEU][hapmap]
rs9862534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap]
rs9871024	1.00[CEU][hapmap]
rs9881860	1.00[CEU][hapmap]

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs9847585	NICN1	cis	Thyroid	GTEx
rs9847585	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs9847585	AMT	cis	Artery Aorta	GTEx
rs9847585	NICN1-AS1	cis	Thyroid	GTEx
rs9847585	WDR6	cis	lung	GTEx
rs9847585	AMT	cis	Thyroid	GTEx
rs9847585	AMT	cis	Artery Tibial	GTEx
rs9847585	WDR6	cis	Nerve Tibial	GTEx
rs9847585	AMT	cis	Esophagus Mucosa	GTEx
rs9847585	AMT	cis	Muscle Skeletal	GTEx
rs9847585	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs9847585	AMT	cis	Esophagus Muscularis	GTEx
rs9847585	WDR6	cis	Muscle Skeletal	GTEx
rs9847585	AMT	cis	Adipose Subcutaneous	GTEx
rs9847585	AMT	cis	lung	GTEx
rs9847585	AMT	cis	Nerve Tibial	GTEx
rs9847585	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs9847585	AMT	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49396400-49418600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49396600-49414400	Weak transcription	Fetal Brain Male	brain
3	chr3:49396800-49438800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:49397000-49415200	Strong transcription	Fetal Stomach	stomach
5	chr3:49397200-49423800	Weak transcription	Fetal Heart	heart
6	chr3:49397400-49416400	Strong transcription	Fetal Intestine Small	intestine
7	chr3:49397800-49415800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:49399000-49448000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:49401600-49415200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:49406000-49416000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:49406000-49416000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:49406000-49445200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:49410600-49421800	Weak transcription	K562	blood
14	chr3:49411000-49416000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:49411000-49434600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:49411200-49418800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:49411200-49423200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:49411200-49423800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:49411800-49417200	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:49412200-49415800	Weak transcription	Stomach Mucosa	stomach
21	chr3:49412400-49415800	Weak transcription	Right Ventricle	heart
22	chr3:49412800-49415000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:49413000-49414400	Weak transcription	Lung	lung
24	chr3:49413000-49414600	Weak transcription	Ovary	ovary
25	chr3:49413000-49414600	Weak transcription	NH-A	brain
26	chr3:49413000-49414800	Weak transcription	Gastric	stomach
27	chr3:49413000-49415000	Weak transcription	NHDF-Ad	bronchial
28	chr3:49413000-49415800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:49413000-49417200	Weak transcription	Small Intestine	intestine
30	chr3:49413000-49418800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:49413000-49421600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:49413000-49422000	Weak transcription	Pancreas	Pancrea
33	chr3:49413000-49423200	Weak transcription	Brain Anterior Caudate	brain
34	chr3:49413000-49423800	Weak transcription	HUVEC	blood vessel
35	chr3:49413200-49414400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:49413200-49414400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:49413200-49414400	Weak transcription	GM12878-XiMat	blood
38	chr3:49413200-49414600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:49413200-49414600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:49413200-49414600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:49413200-49414600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr3:49413200-49414600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:49413200-49414600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr3:49413200-49414600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:49413200-49414600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:49413200-49414600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:49413200-49414600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:49413200-49414600	Weak transcription	Left Ventricle	heart
49	chr3:49413200-49414600	Weak transcription	Spleen	Spleen
50	chr3:49413200-49414600	Weak transcription	A549	lung

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