Variant report

Variant	rs3800654
Chromosome Location	chr7:137439592-137439593
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:137439231..137441193-chr7:137444699..137446812,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10261368	1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13221354	0.81[CEU][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs13235694	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2009990	0.92[CHB][hapmap];0.86[GIH][hapmap]
rs2113426	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2351856	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3778811	1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57370627	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73152535	0.81[EUR][1000 genomes]
rs7797147	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022793	chr7:137187383-137619359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3800654	LRGUK	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:137437600-137439600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr7:137437600-137439800	Enhancers	Fetal Heart	heart
3	chr7:137437800-137439800	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr7:137437800-137440200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr7:137437800-137440400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:137437800-137441000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:137437800-137442000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:137437800-137442600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr7:137438000-137439600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr7:137438000-137439600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:137438000-137439600	Enhancers	Brain Hippocampus Middle	brain
12	chr7:137438000-137439600	Enhancers	NH-A	brain
13	chr7:137438000-137441600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr7:137438000-137442400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr7:137438200-137439600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr7:137438200-137439600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr7:137438400-137439600	Enhancers	Brain Germinal Matrix	brain
18	chr7:137438400-137439600	Enhancers	Fetal Kidney	kidney
19	chr7:137438400-137442400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr7:137438600-137439600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr7:137438600-137440800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr7:137438600-137440800	Enhancers	GM12878-XiMat	blood
23	chr7:137438600-137441800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:137438600-137442400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:137438800-137439600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:137438800-137439600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:137438800-137439600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:137438800-137439600	Bivalent Enhancer	Fetal Stomach	stomach
29	chr7:137438800-137439600	Enhancers	Rectal Smooth Muscle	rectum
30	chr7:137438800-137439600	Enhancers	Right Ventricle	heart
31	chr7:137438800-137439800	Enhancers	Pancreas	Pancrea
32	chr7:137438800-137441200	Enhancers	Fetal Brain Male	brain
33	chr7:137438800-137441600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:137439000-137439600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:137439000-137439600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:137439000-137439600	Enhancers	Spleen	Spleen
37	chr7:137439000-137442400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:137439000-137442600	Enhancers	Osteobl	bone
39	chr7:137439200-137439600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr7:137439200-137439600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr7:137439200-137439600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:137439200-137439600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr7:137439200-137439600	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr7:137439200-137439600	Flanking Active TSS	Fetal Brain Female	brain
45	chr7:137439200-137439600	Enhancers	NHDF-Ad	bronchial
46	chr7:137439200-137439800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:137439200-137440200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:137439400-137439600	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr7:137439400-137439600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:137439400-137439600	Active TSS	Brain Anterior Caudate	brain

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