Variant report

Variant	rs56231305
Chromosome Location	chr7:55979589-55979590
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GBAS-1	chr7:55979309-55979606	NONHSAT120710

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11489729	1.00[ASN][1000 genomes]
rs17172505	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs57580348	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60007968	1.00[ASN][1000 genomes]
rs61193865	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73358448	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73358466	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73358468	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73360334	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73360352	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73360362	1.00[ASN][1000 genomes]
rs73360364	1.00[ASN][1000 genomes]
rs73360369	1.00[ASN][1000 genomes]
rs73360377	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73698917	1.00[ASN][1000 genomes]
rs73698918	1.00[ASN][1000 genomes]
rs73698919	1.00[ASN][1000 genomes]
rs73698972	1.00[ASN][1000 genomes]
rs73698975	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73698976	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv427782	chr7:55703073-56010314	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
8	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription 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	71 gene(s)	inside rSNPs	diseases
10	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers 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	39 gene(s)	inside rSNPs	diseases
11	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
12	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
13	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
14	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv607034	chr7:55974028-56002247	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:55955400-56004200	Weak transcription	Gastric	stomach
2	chr7:55955800-55985800	Weak transcription	Esophagus	oesophagus
3	chr7:55956000-55979600	Weak transcription	Psoas Muscle	Psoas
4	chr7:55956200-55979600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:55956200-55990800	Weak transcription	Thymus	Thymus
6	chr7:55956200-56002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:55956400-55979600	Weak transcription	Brain Angular Gyrus	brain
8	chr7:55956400-55979800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:55956400-55990600	Weak transcription	Brain Anterior Caudate	brain
10	chr7:55956400-55995800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:55956400-55998800	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:55956600-55990800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:55962000-55990000	Weak transcription	HepG2	liver
14	chr7:55962000-55992800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:55966600-55983800	Weak transcription	HUVEC	blood vessel
16	chr7:55966800-55979600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr7:55967600-55995800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr7:55968600-55995000	Weak transcription	HSMM	muscle
19	chr7:55969000-55985600	Weak transcription	Dnd41	blood
20	chr7:55969800-55998200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:55971600-55993400	Weak transcription	Primary B cells from cord blood	blood
22	chr7:55971800-55980200	Weak transcription	Right Ventricle	heart
23	chr7:55971800-55992800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:55973600-55990800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:55973800-55979600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr7:55974200-55994800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:55974400-55995600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr7:55974600-55979800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr7:55974600-55980400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr7:55974800-55979800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr7:55974800-55993200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:55975000-55985600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:55975000-56002000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:55975400-55979600	Weak transcription	Fetal Brain Female	brain
35	chr7:55975400-55980200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr7:55975400-55981000	Weak transcription	Ovary	ovary
37	chr7:55975400-55995000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr7:55975600-55979600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr7:55975600-55979600	Weak transcription	Liver	Liver
40	chr7:55975600-55979600	Weak transcription	Fetal Lung	lung
41	chr7:55975600-55980600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr7:55975600-55982800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr7:55975600-55992800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr7:55975600-55992800	Weak transcription	Fetal Intestine Small	intestine
45	chr7:55975800-55979600	Weak transcription	Fetal Brain Male	brain
46	chr7:55975800-56006800	Weak transcription	Fetal Kidney	kidney
47	chr7:55976800-55994400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr7:55977200-55992400	Weak transcription	Small Intestine	intestine
49	chr7:55977200-55994400	Weak transcription	Hela-S3	cervix
50	chr7:55977800-55997600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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