Variant report

Variant	rs8002180
Chromosome Location	chr13:95922765-95922766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95860458..95862000-chr13:95922105..95923828,2	K562	blood:
2	chr13:95922109..95924473-chr13:95936856..95939759,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12864631	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1970477	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2027445	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389232	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2389233	0.83[EUR][1000 genomes]
rs4360814	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4771910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4773865	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7317112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7322318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991972	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7996898	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524869	0.91[ASN][1000 genomes]
rs9524875	0.94[JPT][hapmap]
rs9584288	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9590228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9590229	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533659	chr13:95757713-96042149	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Blood metabolite levels	24816252	GWAS catalog

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95896200-95923400	Weak transcription	Ovary	ovary
2	chr13:95897000-95927400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr13:95908000-95926600	Weak transcription	Gastric	stomach
4	chr13:95910200-95927400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr13:95913600-95932800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr13:95917000-95931400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr13:95918400-95923400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr13:95918800-95922800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr13:95919000-95922800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr13:95919000-95923200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:95919000-95925600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr13:95919000-95930000	Weak transcription	Esophagus	oesophagus
13	chr13:95919200-95922800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr13:95919400-95923200	Enhancers	HSMM	muscle
15	chr13:95919400-95923600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr13:95919400-95924200	Enhancers	Fetal Stomach	stomach
17	chr13:95919600-95923000	Genic enhancers	K562	blood
18	chr13:95919600-95923400	Enhancers	Osteobl	bone
19	chr13:95919600-95924800	Enhancers	HUVEC	blood vessel
20	chr13:95919800-95923600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr13:95919800-95924600	Enhancers	Rectal Smooth Muscle	rectum
22	chr13:95919800-95928000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr13:95920000-95923600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr13:95920000-95923600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr13:95920200-95922800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:95920200-95923600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr13:95920200-95928800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr13:95920200-95952800	Weak transcription	Aorta	Aorta
29	chr13:95920400-95922800	Weak transcription	Fetal Intestine Large	intestine
30	chr13:95920400-95923000	Enhancers	NHDF-Ad	bronchial
31	chr13:95920400-95923400	Weak transcription	Brain Hippocampus Middle	brain
32	chr13:95920400-95923400	Weak transcription	HepG2	liver
33	chr13:95920400-95923600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr13:95920400-95924400	Enhancers	NH-A	brain
35	chr13:95920400-95927400	Weak transcription	Hela-S3	cervix
36	chr13:95920600-95922800	Weak transcription	Fetal Muscle Leg	muscle
37	chr13:95920600-95928200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr13:95920800-95923200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr13:95920800-95923400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr13:95920800-95925600	Weak transcription	Placenta	Placenta
41	chr13:95921000-95922800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr13:95921000-95923200	Weak transcription	Fetal Kidney	kidney
43	chr13:95921000-95923600	Enhancers	Stomach Smooth Muscle	stomach
44	chr13:95921200-95923000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr13:95921200-95923400	Weak transcription	Fetal Intestine Small	intestine
46	chr13:95921200-95925600	Weak transcription	Lung	lung
47	chr13:95921400-95926200	Weak transcription	Right Atrium	heart
48	chr13:95921600-95922800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr13:95921600-95923600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr13:95921600-95923600	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links