Variant report

Variant	rs2297792
Chromosome Location	chr1:156011444-156011445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155895503..155899194-chr1:156008704..156012136,3	MCF-7	breast:
2	chr1:156006984..156012141-chr1:156021419..156024947,7	MCF-7	breast:
3	chr1:156004095..156006153-chr1:156009168..156012102,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160803	Chromatin interaction
ENSG00000116586	Chromatin interaction
ENSG00000252808	Chromatin interaction
ENSG00000132680	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10908486	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11577179	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11582305	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12032631	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12043212	0.92[CEU][hapmap]
rs12128541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475766	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17381047	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17385065	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1966243	0.82[ASN][1000 genomes]
rs2095402	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364400	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2364401	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2886070	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34126883	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34444588	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34995046	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3820592	0.82[ASN][1000 genomes]
rs4661079	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6668204	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7517202	0.94[AMR][1000 genomes];0.97[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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2297792	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs2297792	SYT11	cis	parietal	SCAN
rs2297792	RIT1	cis	cerebellum	SCAN
rs2297792	YY1AP1	cis	cerebellum	SCAN
rs2297792	PRUNE	cis	cerebellum	SCAN
rs2297792	ROBLD3	cis	parietal	SCAN
rs2297792	PRCC	cis	cerebellum	SCAN
rs2297792	SNX27	cis	parietal	SCAN
rs2297792	SPRR3	cis	parietal	SCAN
rs2297792	UBQLN4	trans	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155991000-156011600	Weak transcription	Colonic Mucosa	Colon
2	chr1:155991200-156020000	Weak transcription	GM12878-XiMat	blood
3	chr1:155996200-156019600	Weak transcription	HMEC	breast
4	chr1:155996200-156022400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:155999800-156020000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:156001200-156022400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:156003200-156012800	Weak transcription	NHLF	lung
8	chr1:156004200-156012200	Weak transcription	Primary B cells from cord blood	blood
9	chr1:156004400-156018600	Strong transcription	Fetal Muscle Leg	muscle
10	chr1:156004800-156017800	Weak transcription	Fetal Brain Male	brain
11	chr1:156005200-156022400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:156005400-156022000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:156005600-156019600	Strong transcription	Fetal Muscle Trunk	muscle
14	chr1:156005600-156020200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:156005600-156021200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:156005600-156021400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:156005800-156013000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:156005800-156013400	Strong transcription	Fetal Thymus	thymus
19	chr1:156005800-156013600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:156005800-156015200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:156005800-156015200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:156005800-156015400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:156005800-156015600	Strong transcription	Liver	Liver
24	chr1:156005800-156020800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:156005800-156021600	Strong transcription	Fetal Intestine Small	intestine
26	chr1:156005800-156022000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:156005800-156022000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:156005800-156022000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:156005800-156022000	Strong transcription	Fetal Stomach	stomach
30	chr1:156006000-156012800	Strong transcription	Thymus	Thymus
31	chr1:156006000-156014800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:156006000-156015000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:156006000-156015400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:156006200-156012800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:156006200-156016800	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:156006400-156015600	Strong transcription	Fetal Brain Female	brain
37	chr1:156006400-156020400	Weak transcription	Psoas Muscle	Psoas
38	chr1:156006600-156015400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:156006600-156015600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:156006800-156013400	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:156006800-156015600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:156006800-156021400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:156007200-156020800	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:156007600-156014000	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr1:156007800-156015000	Weak transcription	HSMM	muscle
46	chr1:156008400-156018800	Weak transcription	Fetal Kidney	kidney
47	chr1:156009000-156013600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:156009000-156022400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:156009200-156012800	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr1:156009200-156015600	Strong transcription	Stomach Smooth Muscle	stomach

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