Variant report

Variant	rs3734444
Chromosome Location	chr6:55739553-55739554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12205334	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2021803	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs3798819	0.81[JPT][hapmap]
rs3807016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715567	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912214	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9464298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2752670	chr6:55614978-55781605	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1032684	chr6:55680473-55766876	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024174	chr6:55713889-55829936	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1029301	chr6:55713889-55834480	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3734444	HMGCLL1	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55733600-55740800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr6:55733600-55740800	Active TSS	Fetal Muscle Leg	muscle
3	chr6:55734200-55740000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:55734200-55740600	Active TSS	Fetal Lung	lung
5	chr6:55734600-55740600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:55734600-55741600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:55734800-55740000	Weak transcription	A549	lung
8	chr6:55735000-55740400	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr6:55735600-55740400	Active TSS	Fetal Intestine Large	intestine
10	chr6:55736200-55740400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:55736400-55740200	Active TSS	Fetal Stomach	stomach
12	chr6:55736400-55740400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:55736400-55740400	Active TSS	Placenta	Placenta
14	chr6:55736600-55740200	Active TSS	Duodenum Mucosa	Duodenum
15	chr6:55737800-55739600	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr6:55738800-55740200	ZNF genes & repeats	Fetal Brain Male	brain
17	chr6:55739000-55739600	Bivalent/Poised TSS	Left Ventricle	heart
18	chr6:55739000-55739600	Active TSS	Right Atrium	heart
19	chr6:55739000-55740000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr6:55739000-55740000	ZNF genes & repeats	Fetal Heart	heart
21	chr6:55739000-55740200	Active TSS	Fetal Kidney	kidney
22	chr6:55739000-55740400	Active TSS	Fetal Intestine Small	intestine
23	chr6:55739000-55740400	Active TSS	Fetal Muscle Trunk	muscle
24	chr6:55739000-55740400	Active TSS	Psoas Muscle	Psoas
25	chr6:55739000-55740400	Active TSS	Right Ventricle	heart
26	chr6:55739000-55740400	Active TSS	Hela-S3	cervix
27	chr6:55739200-55739600	Enhancers	H1 Cell Line	embryonic stem cell
28	chr6:55739200-55739600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:55739200-55739600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:55739200-55739600	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr6:55739200-55739600	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr6:55739200-55739600	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr6:55739200-55740200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr6:55739200-55740800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr6:55739400-55739600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr6:55739400-55739600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr6:55739400-55739800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:55739400-55740000	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr6:55739400-55740400	Active TSS	iPS-20b Cell Line	embryonic stem cell

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