Variant report

Variant	rs578654
Chromosome Location	chr6:165831491-165831492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13195853	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs13198822	0.87[JPT][hapmap]
rs1511747	0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs1849205	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2273404	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs34003270	0.89[ASN][1000 genomes]
rs35535980	0.80[ASN][1000 genomes]
rs3799162	0.80[JPT][hapmap]
rs3818177	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs511096	0.94[ASN][1000 genomes]
rs517550	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs520349	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs578592	0.80[JPT][hapmap]
rs717602	0.82[CHD][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432982	chr6:165528589-165835589	Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv605245	chr6:165542686-165845903	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv1031648	chr6:165544569-165841029	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv432983	chr6:165554403-165851585	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv3417270	chr6:165682773-166023032	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv886928	chr6:165722345-166197889	Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv830863	chr6:165803464-165970091	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv886929	chr6:165821402-165850480	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv886930	chr6:165823608-165850480	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs578654	MLLT4	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:165747600-165853000	Weak transcription	A549	lung
2	chr6:165772000-165835800	Weak transcription	Fetal Kidney	kidney
3	chr6:165788000-165856800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:165791400-165834000	Weak transcription	Brain Anterior Caudate	brain
5	chr6:165806400-165862000	Weak transcription	Right Ventricle	heart
6	chr6:165813800-165831600	Weak transcription	Brain Germinal Matrix	brain
7	chr6:165814200-165853800	Weak transcription	Fetal Lung	lung
8	chr6:165816800-165850600	Weak transcription	Aorta	Aorta
9	chr6:165817000-165835800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:165818400-165835800	Weak transcription	Fetal Brain Male	brain
11	chr6:165818400-165848000	Weak transcription	Spleen	Spleen
12	chr6:165818800-165847200	Weak transcription	Fetal Heart	heart
13	chr6:165822800-165833800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:165823000-165833600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:165823200-165834400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:165824600-165840400	Weak transcription	Ovary	ovary
17	chr6:165825600-165856200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:165826600-165856000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:165827400-165831600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:165827800-165833000	Weak transcription	Adipose Nuclei	Adipose
21	chr6:165829400-165844400	Weak transcription	Hela-S3	cervix
22	chr6:165829800-165837800	Weak transcription	Brain Angular Gyrus	brain
23	chr6:165830000-165833400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:165830400-165831600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:165830600-165833200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:165830800-165832200	Strong transcription	Left Ventricle	heart
27	chr6:165831000-165862800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr6:165831200-165831800	Strong transcription	Placenta	Placenta
29	chr6:165831200-165832000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:165831200-165832200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:165831200-165832200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:165831200-165832200	Strong transcription	HSMM	muscle
33	chr6:165831200-165832800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:165831400-165831600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:165831400-165832000	Strong transcription	HSMMtube	muscle
36	chr6:165831400-165832200	Strong transcription	Fetal Brain Female	brain
37	chr6:165831400-165832200	Strong transcription	Fetal Muscle Leg	muscle
38	chr6:165831400-165832200	Strong transcription	Placenta Amnion	Placenta Amnion

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