Variant report

Variant	rs1397610
Chromosome Location	chr4:120127761-120127762
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120125197..120131905-chr4:120131994..120135569,17	K562	blood:

Variant related genes	Relation type
ENSG00000178636	Chromatin interaction
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10007409	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11737086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511016	0.89[CEU][hapmap]
rs17049975	0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs17049978	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4374607	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66792078	0.81[ASN][1000 genomes]
rs6823331	0.89[CEU][hapmap]
rs6833072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7436509	0.81[ASN][1000 genomes]
rs7440443	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs925387	0.93[JPT][hapmap];0.81[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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1397610	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs1397610	USP53	Cis_1M	lymphoblastoid	RTeQTL
rs1397610	RP11-33B1.1	cis	Muscle Skeletal	GTEx
rs1397610	RP11-33B1.1	cis	Nerve Tibial	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120101000-120132400	Weak transcription	Left Ventricle	heart
2	chr4:120117600-120133200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:120119600-120129600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:120125600-120129200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr4:120125600-120129800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:120125600-120131400	Enhancers	HSMMtube	muscle
7	chr4:120125800-120128600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:120125800-120129000	Enhancers	Osteobl	bone
9	chr4:120125800-120131800	Enhancers	HSMM	muscle
10	chr4:120125800-120132200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:120126000-120128400	Weak transcription	A549	lung
12	chr4:120126000-120129400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:120126200-120128200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:120126200-120131200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:120126200-120132200	Enhancers	NHDF-Ad	bronchial
16	chr4:120126400-120127800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:120126400-120129400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:120126400-120129400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:120126400-120129800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:120126400-120130800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:120126400-120132200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:120126400-120132400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:120126400-120132400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:120126400-120132400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:120126400-120132400	Enhancers	HUVEC	blood vessel
26	chr4:120126400-120132600	Weak transcription	Right Atrium	heart
27	chr4:120126600-120127800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:120126600-120128200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:120126600-120128200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:120126600-120128200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:120126600-120128200	Weak transcription	NHEK	skin
32	chr4:120126600-120128600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr4:120127200-120129000	Enhancers	Fetal Heart	heart
34	chr4:120127200-120129800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:120127400-120127800	Enhancers	Brain Hippocampus Middle	brain
36	chr4:120127400-120128400	Enhancers	Adipose Nuclei	Adipose
37	chr4:120127400-120128800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr4:120127400-120132200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:120127400-120132400	Enhancers	NHLF	lung
40	chr4:120127600-120128000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:120127600-120128000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:120127600-120128600	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr4:120127600-120129200	Enhancers	Fetal Lung	lung
44	chr4:120127600-120130200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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