Variant report

Variant	rs1749976
Chromosome Location	chr13:48730327-48730328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1925747	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2182220	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2406802	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2406804	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2765074	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765075	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942753	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4942754	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4942757	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs607954	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329629	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7988534	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7989671	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7993868	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7994141	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7995410	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9534969	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9534978	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9534979	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9534983	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9534988	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[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	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1047140	chr13:48703732-48765860	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv541767	chr13:48703732-48765860	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1749976	SERP2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48717400-48733200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:48722400-48730600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr13:48723200-48730600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr13:48723800-48730400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr13:48724200-48738200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr13:48726200-48731600	Enhancers	Placenta	Placenta
7	chr13:48726400-48730400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr13:48726400-48733600	Weak transcription	Esophagus	oesophagus
9	chr13:48726400-48735400	Weak transcription	Lung	lung
10	chr13:48726600-48731600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:48726600-48732000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr13:48727400-48730400	Enhancers	NHEK	skin
13	chr13:48727600-48731200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr13:48728200-48731200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr13:48728400-48730400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr13:48728400-48731200	Enhancers	HMEC	breast
17	chr13:48728400-48731600	Enhancers	Primary T cells from cord blood	blood
18	chr13:48728600-48731000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr13:48728600-48733600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr13:48728600-48735400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr13:48728800-48730400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr13:48728800-48730800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr13:48728800-48730800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr13:48728800-48731000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr13:48728800-48731000	Enhancers	Primary hematopoietic stem cells	blood
26	chr13:48728800-48731000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr13:48728800-48731000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:48728800-48731000	Enhancers	Adipose Nuclei	Adipose
29	chr13:48728800-48731200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr13:48728800-48731200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr13:48729000-48730800	Enhancers	Small Intestine	intestine
32	chr13:48729000-48731200	Enhancers	Hela-S3	cervix
33	chr13:48729200-48730600	Enhancers	HSMM	muscle
34	chr13:48729200-48730800	Enhancers	HepG2	liver
35	chr13:48729200-48733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr13:48729400-48730400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr13:48729400-48730400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr13:48729400-48730400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr13:48729400-48730400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr13:48729400-48730400	Enhancers	A549	lung
41	chr13:48729400-48730800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr13:48729400-48731000	Enhancers	Thymus	Thymus
43	chr13:48729400-48731000	Enhancers	HUVEC	blood vessel
44	chr13:48729400-48734000	Enhancers	Fetal Thymus	thymus
45	chr13:48729800-48730400	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr13:48729800-48730600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr13:48729800-48731000	Enhancers	NH-A	brain
48	chr13:48729800-48731200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr13:48730000-48730400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr13:48730000-48730400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links