Variant report

Variant	rs11688977
Chromosome Location	chr2:38896631-38896632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
2	chr2:38867821..38870295-chr2:38895225..38897165,2	K562	blood:
3	chr2:38895186..38897690-chr2:38903114..38905637,2	K562	blood:
4	chr2:38893888..38897011-chr2:38898419..38901251,3	K562	blood:
5	chr2:38825670..38832919-chr2:38891527..38903424,21	K562	blood:
6	chr2:38891821..38893324-chr2:38896247..38899182,2	K562	blood:
7	chr2:38895714..38897624-chr2:38914031..38916538,2	K562	blood:
8	chr2:38884282..38886148-chr2:38894534..38896833,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HNRPLL-2	chr2:38896481-38896680	ENSG00000232518.1

No data

Variant related genes	Relation type
ENSG00000235586	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000232518	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11689051	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478924	0.93[EUR][1000 genomes]
rs12712609	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011383	0.94[EUR][1000 genomes]
rs13029674	0.92[EUR][1000 genomes]
rs13387464	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425086	0.94[EUR][1000 genomes]
rs2373424	0.93[EUR][1000 genomes]
rs28551538	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs34533539	0.86[EUR][1000 genomes]
rs3821023	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670263	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670882	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670883	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6707543	0.86[EUR][1000 genomes]
rs6732137	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6736380	0.86[EUR][1000 genomes]
rs6744400	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6761563	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7571326	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7574493	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588762	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590750	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590835	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590926	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597535	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv873883	chr2:38881106-38932777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38893800-38897400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:38893800-38903000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:38894000-38897400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:38894000-38903000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:38894000-38903000	Weak transcription	Lung	lung
6	chr2:38894000-38904200	Weak transcription	Esophagus	oesophagus
7	chr2:38894000-38904400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:38894000-38917600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:38894200-38897400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:38894200-38897600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:38894200-38898200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:38894200-38903200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:38894200-38903400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:38894200-38904000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:38894200-38904000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:38894200-38904000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:38894200-38904600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:38894200-38906800	Weak transcription	Brain Angular Gyrus	brain
19	chr2:38894200-38919000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:38894400-38897400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:38894400-38897400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:38894400-38897400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:38894400-38897400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:38894400-38897400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:38894400-38897400	Weak transcription	A549	lung
26	chr2:38894400-38897600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:38894400-38903000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:38894400-38903000	Weak transcription	Fetal Kidney	kidney
29	chr2:38894400-38903000	Weak transcription	Fetal Lung	lung
30	chr2:38894400-38903000	Weak transcription	Left Ventricle	heart
31	chr2:38894400-38903000	Weak transcription	Thymus	Thymus
32	chr2:38894400-38903000	Weak transcription	NHLF	lung
33	chr2:38894400-38903200	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:38894400-38903800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:38894400-38903800	Weak transcription	Right Ventricle	heart
36	chr2:38894400-38904000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:38894400-38904000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:38894400-38904000	Weak transcription	Placenta	Placenta
39	chr2:38894400-38908600	Weak transcription	Brain Anterior Caudate	brain
40	chr2:38894400-38910400	Weak transcription	Psoas Muscle	Psoas
41	chr2:38894400-38917600	Weak transcription	NHDF-Ad	bronchial
42	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
43	chr2:38894600-38902800	Weak transcription	Fetal Stomach	stomach
44	chr2:38894600-38903000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:38894600-38903000	Weak transcription	Adipose Nuclei	Adipose
46	chr2:38894600-38903000	Weak transcription	Fetal Thymus	thymus
47	chr2:38894600-38903000	Weak transcription	Ovary	ovary
48	chr2:38894600-38903000	Weak transcription	Spleen	Spleen
49	chr2:38894600-38903200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:38894600-38903200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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