Variant report

Variant	rs41424948
Chromosome Location	chr1:165413042-165413043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs100537	0.93[ASW][hapmap];0.89[CEU][hapmap];0.84[TSI][hapmap]
rs10918178	0.81[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1128977	0.81[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4657437	0.86[AMR][1000 genomes]
rs61800587	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61800588	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61800589	0.84[EUR][1000 genomes]
rs6676763	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41424948	TMCO1	cis	parietal	SCAN
rs41424948	ARHGAP30	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165412200-165414800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:165412400-165413200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:165412400-165413400	Flanking Active TSS	Fetal Muscle Trunk	muscle
4	chr1:165412400-165413400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr1:165412400-165414800	Active TSS	Brain Anterior Caudate	brain
6	chr1:165412600-165413200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
7	chr1:165412600-165413200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
8	chr1:165412600-165413200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
9	chr1:165412600-165413400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
10	chr1:165412600-165413600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
11	chr1:165412600-165413600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
12	chr1:165412600-165413800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:165412600-165414000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
14	chr1:165412600-165414000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:165412600-165414000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:165412600-165414200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:165412600-165414200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:165412800-165413200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:165412800-165413200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:165412800-165413200	Flanking Active TSS	Fetal Lung	lung
21	chr1:165412800-165413400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
22	chr1:165412800-165413400	Enhancers	Adipose Nuclei	Adipose
23	chr1:165412800-165413400	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr1:165412800-165413400	Enhancers	Right Atrium	heart
25	chr1:165412800-165413800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:165412800-165413800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
27	chr1:165412800-165413800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr1:165412800-165414000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:165412800-165414000	Bivalent Enhancer	Colon Smooth Muscle	Colon
30	chr1:165412800-165414000	Enhancers	Left Ventricle	heart
31	chr1:165412800-165414400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
32	chr1:165412800-165414600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:165412800-165414800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:165412800-165414800	Active TSS	Brain Substantia Nigra	brain
35	chr1:165413000-165413200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
36	chr1:165413000-165413200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
37	chr1:165413000-165413200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
38	chr1:165413000-165413200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
39	chr1:165413000-165413200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
40	chr1:165413000-165413200	Weak transcription	Pancreas	Pancrea
41	chr1:165413000-165413200	Flanking Active TSS	Right Ventricle	heart
42	chr1:165413000-165413200	Bivalent Enhancer	Small Intestine	intestine
43	chr1:165413000-165413200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
44	chr1:165413000-165413400	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr1:165413000-165413400	Flanking Active TSS	Psoas Muscle	Psoas
46	chr1:165413000-165413800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:165413000-165413800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:165413000-165413800	Bivalent/Poised TSS	Fetal Brain Female	brain
49	chr1:165413000-165413800	Enhancers	Fetal Heart	heart
50	chr1:165413000-165413800	Weak transcription	Lung	lung

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