Variant report

Variant	rs614373
Chromosome Location	chr1:58714427-58714428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:58711426..58714604-chr1:58717021..58720890,3	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12124585	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs474294	0.85[CEU][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs4912185	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs542511	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs576103	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs590047	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs647762	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7537039	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv546307	chr1:58707111-58733050	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv546308	chr1:58714427-58743499	Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs614373	TM2D1	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58713000-58716800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
2	chr1:58713200-58714600	Bivalent/Poised TSS	Fetal Brain Female	brain
3	chr1:58713600-58714600	Bivalent Enhancer	Liver	Liver
4	chr1:58713600-58715200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
5	chr1:58713800-58714600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
6	chr1:58713800-58714600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
7	chr1:58713800-58714600	Enhancers	Left Ventricle	heart
8	chr1:58713800-58715000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:58713800-58715200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:58713800-58715600	Enhancers	Rectal Smooth Muscle	rectum
11	chr1:58713800-58715800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:58713800-58716000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
13	chr1:58714000-58714600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:58714000-58714600	Active TSS	Brain Angular Gyrus	brain
15	chr1:58714000-58714800	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
16	chr1:58714000-58715000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
17	chr1:58714000-58715200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:58714000-58715200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
19	chr1:58714200-58714600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
20	chr1:58714200-58714600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:58714200-58714600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
22	chr1:58714200-58714600	Bivalent Enhancer	Fetal Heart	heart
23	chr1:58714200-58714800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr1:58714200-58714800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
25	chr1:58714200-58714800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
26	chr1:58714200-58714800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:58714200-58714800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:58714200-58715000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:58714200-58715000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:58714200-58715200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
31	chr1:58714200-58715400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
32	chr1:58714200-58715800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
33	chr1:58714200-58716200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
34	chr1:58714200-58716200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:58714200-58716200	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr1:58714400-58714600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
37	chr1:58714400-58714600	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
38	chr1:58714400-58714600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
39	chr1:58714400-58714600	Flanking Active TSS	Fetal Brain Male	brain
40	chr1:58714400-58714600	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
41	chr1:58714400-58714600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
42	chr1:58714400-58714800	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
43	chr1:58714400-58714800	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:58714400-58714800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
45	chr1:58714400-58714800	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:58714400-58714800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
47	chr1:58714400-58714800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
48	chr1:58714400-58714800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
49	chr1:58714400-58715000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
50	chr1:58714400-58715200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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