Variant report

Variant	rs2297775
Chromosome Location	chr1:155735012-155735013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155730706..155733174-chr1:155733951..155736426,2	K562	blood:
2	chr1:155733230..155735390-chr1:155735568..155737501,2	K562	blood:
3	chr1:155733230..155735390-chr1:155735568..155738519,3	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10908471	0.84[CEU][hapmap]
rs10908479	0.88[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10908480	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10908481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10908482	0.91[ASN][1000 genomes]
rs11264387	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs11264409	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11264410	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264413	0.82[ASN][1000 genomes]
rs12024187	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12035524	0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap]
rs12040894	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12047756	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12081192	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12407800	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12563627	0.80[JPT][hapmap]
rs12744132	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1556488	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs1749405	0.80[JPT][hapmap]
rs2016251	0.86[MEX][hapmap]
rs2048431	0.88[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap]
rs2175391	0.88[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs2282301	0.82[MEX][hapmap]
rs28582361	0.92[ASN][1000 genomes]
rs28662267	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2948071	0.92[ASN][1000 genomes]
rs2948072	0.93[ASN][1000 genomes]
rs2985707	0.96[ASN][1000 genomes]
rs2993207	0.80[JPT][hapmap]
rs348196	0.85[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]
rs3738590	0.88[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap]
rs3820594	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3892792	0.84[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs4278368	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4661175	0.83[MEX][hapmap]
rs475550	0.88[CEU][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs488079	0.80[JPT][hapmap]
rs490608	0.86[ASN][1000 genomes]
rs625658	0.80[JPT][hapmap]
rs6427286	0.95[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs6427287	0.94[ASN][1000 genomes]
rs6657670	0.82[ASN][1000 genomes]
rs6662953	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6665227	0.91[ASN][1000 genomes]
rs6667652	0.82[MEX][hapmap]
rs670876	0.85[CHB][hapmap]
rs678157	0.82[JPT][hapmap]
rs708611	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs729022	0.80[JPT][hapmap];0.86[MEX][hapmap]
rs7541060	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs7550402	0.94[ASN][1000 genomes]
rs821551	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs822025	0.93[ASN][1000 genomes]
rs822478	0.90[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs822490	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs822505	0.80[JPT][hapmap]
rs822508	0.80[JPT][hapmap];0.87[MEX][hapmap]
rs822527	1.00[ASN][1000 genomes]
rs860295	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs867549	0.82[MEX][hapmap]
rs867550	0.82[MEX][hapmap]
rs915181	0.82[MEX][hapmap]
rs9426933	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers 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	43 gene(s)	inside rSNPs	diseases
4	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv946423	chr1:155732243-155737328	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2297775	SPRR3	cis	parietal	SCAN
rs2297775	YY1AP1	cis	parietal	SCAN
rs2297775	RIT1	cis	Thyroid	GTEx
rs2297775	ROBLD3	cis	parietal	SCAN
rs2297775	GPATCH4	cis	parietal	SCAN
rs2297775	GON4L	Cis_1M	lymphoblastoid	RTeQTL
rs2297775	ADAM15	cis	multi-tissue	Pritchard
rs2297775	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs2297775	YY1AP1	cis	cerebellum	SCAN
rs2297775	RIT1	cis	cerebellum	SCAN
rs2297775	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs2297775	PRUNE	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155715400-155739200	Weak transcription	Fetal Heart	heart
2	chr1:155715400-155789200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:155715600-155764600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:155716000-155793400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:155716600-155781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:155717200-155761000	Strong transcription	Fetal Stomach	stomach
7	chr1:155717400-155795800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:155717600-155750200	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr1:155720200-155745400	Strong transcription	Fetal Muscle Leg	muscle
10	chr1:155720200-155748600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:155720200-155748800	Strong transcription	Duodenum Mucosa	Duodenum
12	chr1:155720200-155748800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr1:155720200-155749000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:155720200-155749600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:155720200-155750200	Strong transcription	Primary T cells from cord blood	blood
16	chr1:155720200-155750600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:155720200-155755800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:155720200-155756200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:155720200-155756600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:155720200-155798200	Strong transcription	Fetal Thymus	thymus
21	chr1:155720200-155803600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:155720400-155743200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr1:155720400-155743200	Strong transcription	Thymus	Thymus
24	chr1:155720400-155750200	Strong transcription	Adipose Nuclei	Adipose
25	chr1:155720400-155750400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:155720400-155750600	Strong transcription	Dnd41	blood
27	chr1:155720400-155755600	Strong transcription	Placenta	Placenta
28	chr1:155720400-155756400	Strong transcription	Liver	Liver
29	chr1:155720400-155760800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr1:155720400-155796800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:155720600-155735800	Strong transcription	Rectal Smooth Muscle	rectum
32	chr1:155720600-155743200	Strong transcription	Fetal Brain Female	brain
33	chr1:155720600-155743600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:155720600-155757200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:155720800-155737200	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr1:155720800-155741800	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:155720800-155742800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:155720800-155743000	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr1:155720800-155747600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:155720800-155749000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:155721000-155748800	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:155722800-155740800	Strong transcription	Fetal Kidney	kidney
43	chr1:155725000-155748600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:155725200-155740200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:155726000-155743000	Strong transcription	Lung	lung
46	chr1:155726000-155747400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:155726200-155737000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:155727200-155754200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:155728600-155747600	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr1:155728800-155736800	Strong transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links