Variant report

Variant	rs11860448
Chromosome Location	chr16:81346264-81346265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GCSH-1	chr16:81345111-81348378	NONHSAT143942
2	lnc-GCSH-1	chr16:81344336-81347028	ENSG00000260495.1

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11150382	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11150383	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11643932	0.83[AFR][1000 genomes]
rs12445484	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12447470	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12918775	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12920172	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35378839	0.86[AFR][1000 genomes]
rs7196957	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7202734	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9934557	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[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	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
5	nsv522890	chr16:81341363-81348396	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81328000-81347000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr16:81328200-81347000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr16:81328600-81347000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr16:81330600-81347200	Weak transcription	Gastric	stomach
5	chr16:81331600-81347000	Weak transcription	Right Ventricle	heart
6	chr16:81331800-81346400	Weak transcription	Brain Anterior Caudate	brain
7	chr16:81332200-81346400	Weak transcription	Fetal Stomach	stomach
8	chr16:81332400-81346400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr16:81333200-81346400	Weak transcription	Brain Germinal Matrix	brain
10	chr16:81334400-81346600	Weak transcription	Colon Smooth Muscle	Colon
11	chr16:81334600-81347200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr16:81335600-81346400	Weak transcription	Primary T cells from cord blood	blood
13	chr16:81337600-81347000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr16:81338000-81346400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr16:81338200-81346600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr16:81338400-81347000	Weak transcription	Spleen	Spleen
17	chr16:81338400-81347200	Weak transcription	Primary B cells from cord blood	blood
18	chr16:81338400-81347400	Weak transcription	Aorta	Aorta
19	chr16:81338600-81346600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr16:81338600-81347400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr16:81338800-81346600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr16:81339600-81346600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr16:81340000-81346400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr16:81340600-81346400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr16:81340800-81347000	Weak transcription	Fetal Muscle Leg	muscle
26	chr16:81341600-81346400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr16:81342000-81346400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr16:81342000-81347000	Weak transcription	Fetal Lung	lung
29	chr16:81342200-81346400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr16:81342200-81346400	Weak transcription	Small Intestine	intestine
31	chr16:81342200-81346600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr16:81342200-81346800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr16:81342600-81346600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr16:81343200-81347000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr16:81343200-81347000	Weak transcription	NHDF-Ad	bronchial
36	chr16:81343200-81347200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr16:81343200-81347400	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr16:81343400-81346400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr16:81343600-81346400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr16:81343600-81347200	Weak transcription	Pancreas	Pancrea
41	chr16:81344000-81347200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr16:81344000-81347200	Weak transcription	Placenta	Placenta
43	chr16:81344200-81346600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr16:81344200-81347000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr16:81344200-81347000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr16:81344200-81347000	Weak transcription	K562	blood
47	chr16:81344400-81347000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr16:81344400-81347000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr16:81344400-81347200	Weak transcription	A549	lung
50	chr16:81344600-81347000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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