Variant report

Variant	rs924900
Chromosome Location	chr7:55973939-55973940
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GBAS-1	chr7:55973882-55974072	NONHSAT120710

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10257154	0.91[ASN][1000 genomes]
rs13222500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13222893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13223226	0.81[ASN][1000 genomes]
rs13232723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13232756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13233754	0.85[CHB][hapmap]
rs13238152	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs13238424	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs13239795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13243072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13243725	0.82[EUR][1000 genomes]
rs13340526	0.82[EUR][1000 genomes]
rs17172501	0.85[CHB][hapmap]
rs2242510	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs28498258	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34015089	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34114241	0.94[AMR][1000 genomes]
rs34279655	0.92[CHB][hapmap]
rs34304703	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34719181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34719521	0.82[EUR][1000 genomes]
rs34874704	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35092795	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35160834	0.82[EUR][1000 genomes]
rs35208675	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35210477	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs35304280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35811559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735066	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs3813504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4360246	0.82[EUR][1000 genomes]
rs56917729	0.82[EUR][1000 genomes]
rs71543767	0.84[EUR][1000 genomes]
rs71543770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71543773	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73343714	0.82[EUR][1000 genomes]
rs73343719	0.82[EUR][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	esv3419807	chr7:55969758-55974056	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs924900	PSPH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:55955400-56004200	Weak transcription	Gastric	stomach
2	chr7:55955800-55975000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:55955800-55985800	Weak transcription	Esophagus	oesophagus
4	chr7:55956000-55974200	Weak transcription	Aorta	Aorta
5	chr7:55956000-55979600	Weak transcription	Psoas Muscle	Psoas
6	chr7:55956200-55974000	Weak transcription	Ovary	ovary
7	chr7:55956200-55974200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr7:55956200-55975200	Weak transcription	HSMMtube	muscle
9	chr7:55956200-55979400	Weak transcription	Primary T cells from cord blood	blood
10	chr7:55956200-55979600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr7:55956200-55990800	Weak transcription	Thymus	Thymus
12	chr7:55956200-56002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:55956400-55974400	Weak transcription	Adipose Nuclei	Adipose
14	chr7:55956400-55974800	Weak transcription	Fetal Kidney	kidney
15	chr7:55956400-55975000	Weak transcription	Liver	Liver
16	chr7:55956400-55979000	Weak transcription	Brain Substantia Nigra	brain
17	chr7:55956400-55979600	Weak transcription	Brain Angular Gyrus	brain
18	chr7:55956400-55979800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:55956400-55990600	Weak transcription	Brain Anterior Caudate	brain
20	chr7:55956400-55995800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:55956400-55998800	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:55956600-55974600	Weak transcription	Fetal Brain Male	brain
23	chr7:55956600-55979400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr7:55956600-55990800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr7:55961800-55979400	Weak transcription	Spleen	Spleen
26	chr7:55962000-55974000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr7:55962000-55990000	Weak transcription	HepG2	liver
28	chr7:55962000-55992800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:55962400-55974600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:55962600-55977800	Weak transcription	Fetal Heart	heart
31	chr7:55964600-55974600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:55966000-55974200	Weak transcription	Brain Hippocampus Middle	brain
33	chr7:55966400-55974000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr7:55966400-55974000	Weak transcription	Fetal Muscle Leg	muscle
35	chr7:55966600-55983800	Weak transcription	HUVEC	blood vessel
36	chr7:55966800-55979600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr7:55967600-55995800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr7:55968000-55975200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr7:55968200-55975200	Weak transcription	Fetal Intestine Small	intestine
40	chr7:55968400-55974000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:55968600-55995000	Weak transcription	HSMM	muscle
42	chr7:55969000-55974400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:55969000-55975000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr7:55969000-55985600	Weak transcription	Dnd41	blood
45	chr7:55969200-55974000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr7:55969400-55974000	Weak transcription	Brain Germinal Matrix	brain
47	chr7:55969600-55974200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr7:55969600-55974200	Weak transcription	Fetal Thymus	thymus
49	chr7:55969600-55974800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr7:55969600-55974800	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links