Variant report

Variant	rs28846144
Chromosome Location	chr3:98523345-98523346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10226213	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10227257	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10227292	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10227294	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10227906	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10231906	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10242107	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10246993	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10258530	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10272544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10272922	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10273938	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10952261	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12673426	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13438625	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2204317	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2222524	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35189910	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35550652	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35977714	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36199992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56338308	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57551458	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59972370	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9640275	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
2	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
4	chr3:98502200-98523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:98502400-98523800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:98503400-98576400	Weak transcription	Gastric	stomach
7	chr3:98503600-98523800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
9	chr3:98505000-98525600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:98505400-98523800	Weak transcription	Pancreas	Pancrea
11	chr3:98505400-98524400	Weak transcription	Thymus	Thymus
12	chr3:98505800-98524600	Weak transcription	Psoas Muscle	Psoas
13	chr3:98506400-98524400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:98506800-98523800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:98507800-98529000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:98508000-98524600	Weak transcription	GM12878-XiMat	blood
17	chr3:98508200-98524600	Weak transcription	Fetal Heart	heart
18	chr3:98513000-98524400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:98513400-98523800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
22	chr3:98513800-98524400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:98513800-98525400	Weak transcription	Esophagus	oesophagus
24	chr3:98513800-98526000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:98515400-98524400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:98515400-98524600	Weak transcription	Placenta	Placenta
27	chr3:98515600-98523800	Weak transcription	Aorta	Aorta
28	chr3:98515600-98523800	Weak transcription	Liver	Liver
29	chr3:98515600-98533400	Weak transcription	Fetal Intestine Small	intestine
30	chr3:98516800-98528600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
32	chr3:98517000-98523800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:98517000-98523800	Weak transcription	Brain Angular Gyrus	brain
34	chr3:98517000-98524400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:98517000-98525400	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:98517200-98531400	Weak transcription	Hela-S3	cervix
37	chr3:98518000-98523800	Weak transcription	K562	blood
38	chr3:98518600-98524200	Weak transcription	Fetal Brain Female	brain
39	chr3:98518600-98524600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:98518800-98523600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:98518800-98523800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:98518800-98523800	Weak transcription	Fetal Thymus	thymus
43	chr3:98519600-98524400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:98519600-98524400	Weak transcription	HepG2	liver
45	chr3:98519800-98523600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:98519800-98523800	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:98520000-98523600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:98520200-98523400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:98520200-98523800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:98520200-98523800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links