Variant report

Variant	rs2705515
Chromosome Location	chr3:112321818-112321819
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:112321767-112321998	ProgFib	skin:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC35A5-1	chr3:112315667-112322287	XLOC_002759

Variant related genes	Relation type
ENSG00000272761	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1105938	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1155073	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1398091	0.85[AMR][1000 genomes]
rs1488259	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1533159	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1601852	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1814052	0.87[ASN][1000 genomes]
rs1873572	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2137199	0.85[AMR][1000 genomes]
rs2171514	0.87[ASN][1000 genomes]
rs2292442	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633574	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2633575	0.87[ASN][1000 genomes]
rs2633579	0.86[ASN][1000 genomes]
rs2633588	0.87[ASN][1000 genomes]
rs2633589	0.87[ASN][1000 genomes]
rs2638013	0.87[ASN][1000 genomes]
rs2638015	0.87[ASN][1000 genomes]
rs2638019	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638023	0.87[ASN][1000 genomes]
rs2638026	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638028	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638029	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638032	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638035	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638039	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668215	0.89[AMR][1000 genomes]
rs2668219	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705505	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2705507	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2705518	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705519	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705521	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705522	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705525	0.87[ASN][1000 genomes]
rs2705541	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2705548	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2705552	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2705556	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705560	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705562	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2705564	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705565	0.86[ASN][1000 genomes]
rs2933134	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2933135	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933137	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2942061	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952319	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952320	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952324	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2952325	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2969895	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2969896	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2971204	0.86[ASN][1000 genomes]
rs3112268	0.86[ASN][1000 genomes]
rs728568	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751875	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766969	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998036	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers 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	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
2	chr3:112281800-112325400	Weak transcription	Gastric	stomach
3	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
5	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:112298600-112325200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:112300200-112331000	Weak transcription	Lung	lung
11	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
12	chr3:112302600-112322800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:112302800-112324200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:112303600-112322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:112303800-112324200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:112305000-112324200	Weak transcription	Fetal Brain Male	brain
17	chr3:112305200-112323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:112305200-112323600	Weak transcription	Brain Substantia Nigra	brain
19	chr3:112305400-112323400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:112305400-112324000	Weak transcription	Brain Anterior Caudate	brain
21	chr3:112305400-112330400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:112305600-112324200	Weak transcription	Fetal Kidney	kidney
23	chr3:112305800-112334800	Weak transcription	Aorta	Aorta
24	chr3:112307400-112329000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:112311600-112330600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:112311600-112331000	Weak transcription	Psoas Muscle	Psoas
27	chr3:112312400-112324200	Weak transcription	Ovary	ovary
28	chr3:112312400-112325200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:112312400-112326800	Weak transcription	Fetal Lung	lung
30	chr3:112312400-112331000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:112312600-112322000	Weak transcription	HUVEC	blood vessel
32	chr3:112312600-112323000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:112312600-112323400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:112312600-112323600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:112312600-112323600	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:112312600-112324200	Weak transcription	Brain Angular Gyrus	brain
37	chr3:112312600-112330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:112312600-112346200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:112312600-112347200	Weak transcription	Fetal Intestine Large	intestine
40	chr3:112316000-112327400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:112316200-112323600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:112316200-112342800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:112316400-112323400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:112316400-112333600	Weak transcription	A549	lung
45	chr3:112316600-112337600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:112316800-112323000	Weak transcription	NHDF-Ad	bronchial
47	chr3:112316800-112323600	Weak transcription	Primary T cells from cord blood	blood
48	chr3:112317000-112324200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:112317200-112322600	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr3:112317600-112322600	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links