Variant report

Variant	rs28767320
Chromosome Location	chr15:42488174-42488175
allele	G/T
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	PAX5	chr15:42488008-42488186	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
VPS39	TF binding region

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs12915387	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1616957	0.88[ASN][1000 genomes]
rs1619537	0.88[ASN][1000 genomes]
rs1626437	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1630294	0.84[ASN][1000 genomes]
rs1678987	0.84[ASN][1000 genomes]
rs1678988	0.84[ASN][1000 genomes]
rs1678989	0.84[ASN][1000 genomes]
rs1678990	0.84[ASN][1000 genomes]
rs1678995	0.94[ASN][1000 genomes]
rs1678996	0.94[ASN][1000 genomes]
rs1679000	0.94[ASN][1000 genomes]
rs1679001	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1679008	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1703748	0.94[ASN][1000 genomes]
rs1703751	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1703753	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1712390	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1712391	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1712397	0.88[ASN][1000 genomes]
rs1712406	0.88[ASN][1000 genomes]
rs1712407	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1712417	0.84[ASN][1000 genomes]
rs1712420	0.84[ASN][1000 genomes]
rs1712422	0.88[ASN][1000 genomes]
rs1712442	0.88[ASN][1000 genomes]
rs2412671	0.94[ASN][1000 genomes]
rs2412674	0.88[ASN][1000 genomes]
rs2620378	0.94[ASN][1000 genomes]
rs2620379	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2620380	0.94[ASN][1000 genomes]
rs2620381	0.87[ASN][1000 genomes]
rs2620383	0.88[ASN][1000 genomes]
rs2663092	0.94[ASN][1000 genomes]
rs2663093	0.84[AMR][1000 genomes]
rs2663096	0.88[ASN][1000 genomes]
rs2677751	0.94[ASN][1000 genomes]
rs2928333	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4583208	0.86[EUR][1000 genomes]
rs4924633	0.84[ASN][1000 genomes]
rs4924635	0.80[ASN][1000 genomes]
rs4924636	0.84[ASN][1000 genomes]
rs583541	0.90[ASN][1000 genomes]
rs588695	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs590540	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs593910	0.94[ASN][1000 genomes]
rs598441	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599316	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs602270	0.94[ASN][1000 genomes]
rs603468	0.88[ASN][1000 genomes]
rs607959	0.88[ASN][1000 genomes]
rs609660	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs613090	0.88[ASN][1000 genomes]
rs613131	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs613157	0.94[ASN][1000 genomes]
rs614733	0.94[ASN][1000 genomes]
rs614774	0.94[ASN][1000 genomes]
rs615023	0.92[ASN][1000 genomes]
rs616071	0.94[ASN][1000 genomes]
rs618161	0.88[ASN][1000 genomes]
rs621365	0.94[ASN][1000 genomes]
rs627478	0.94[ASN][1000 genomes]
rs629255	0.94[ASN][1000 genomes]
rs633310	0.84[ASN][1000 genomes]
rs633483	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs635617	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs635669	0.94[ASN][1000 genomes]
rs635690	0.94[ASN][1000 genomes]
rs635919	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636604	0.94[ASN][1000 genomes]
rs637445	0.94[ASN][1000 genomes]
rs638240	0.88[ASN][1000 genomes]
rs641119	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs644627	0.94[ASN][1000 genomes]
rs645304	0.94[ASN][1000 genomes]
rs647581	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs648720	0.90[ASN][1000 genomes]
rs650910	0.94[ASN][1000 genomes]
rs652192	0.88[ASN][1000 genomes]
rs659354	0.88[ASN][1000 genomes]
rs660033	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs663454	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs665262	0.94[ASN][1000 genomes]
rs665718	0.94[ASN][1000 genomes]
rs668973	0.94[ASN][1000 genomes]
rs670329	0.94[ASN][1000 genomes]
rs670421	0.94[ASN][1000 genomes]
rs672946	0.94[ASN][1000 genomes]
rs677845	0.94[ASN][1000 genomes]
rs677895	0.94[ASN][1000 genomes]
rs683227	0.88[ASN][1000 genomes]
rs683579	0.88[ASN][1000 genomes]
rs685521	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7181577	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8023923	0.88[ASN][1000 genomes]
rs8031735	0.84[ASN][1000 genomes]
rs8108	0.88[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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42460000-42499200	Weak transcription	A549	lung
2	chr15:42460000-42499800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:42466000-42498800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:42475000-42499200	Weak transcription	Stomach Mucosa	stomach
5	chr15:42476800-42499600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:42477200-42497800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:42478400-42498600	Weak transcription	Gastric	stomach
8	chr15:42480200-42496000	Weak transcription	Esophagus	oesophagus
9	chr15:42480400-42498600	Weak transcription	Small Intestine	intestine
10	chr15:42480400-42498800	Weak transcription	Right Ventricle	heart
11	chr15:42480600-42491400	Weak transcription	Psoas Muscle	Psoas
12	chr15:42480600-42496000	Weak transcription	Spleen	Spleen
13	chr15:42481200-42499800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:42481400-42489600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:42481600-42497600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:42481600-42497600	Weak transcription	HUVEC	blood vessel
17	chr15:42481600-42498600	Weak transcription	Fetal Brain Male	brain
18	chr15:42482800-42499400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:42483200-42499400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:42483400-42489600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:42483400-42498600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:42483400-42498600	Weak transcription	Fetal Kidney	kidney
23	chr15:42483600-42497600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr15:42483600-42498600	Weak transcription	Brain Substantia Nigra	brain
25	chr15:42483600-42498600	Weak transcription	K562	blood
26	chr15:42483600-42499200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:42483800-42489600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:42483800-42489600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:42483800-42489600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:42483800-42489600	Weak transcription	Colon Smooth Muscle	Colon
31	chr15:42483800-42492600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:42483800-42499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:42484000-42489600	Weak transcription	Placenta	Placenta
34	chr15:42484000-42489800	Weak transcription	NHDF-Ad	bronchial
35	chr15:42484000-42499200	Weak transcription	HMEC	breast
36	chr15:42484200-42489600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:42484200-42490000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:42484200-42491600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr15:42484200-42493400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr15:42484400-42489600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:42484400-42489600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:42484400-42489600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:42484400-42489600	Weak transcription	NH-A	brain
44	chr15:42484400-42489800	Weak transcription	HSMM	muscle
45	chr15:42484400-42490000	Weak transcription	Ovary	ovary
46	chr15:42484400-42495800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:42484400-42499400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr15:42484800-42488800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:42484800-42489000	Weak transcription	Liver	Liver
50	chr15:42484800-42489000	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links