Variant report

Variant	rs2421325
Chromosome Location	chr1:170512277-170512278
allele	C/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	MAFF	chr1:170512203-170512342	HepG2	liver:	n/a	chr1:170512232-170512250
2	MAFK	chr1:170512117-170512419	HepG2	liver:	n/a	chr1:170512234-170512249
3	MAFK	chr1:170511978-170512510	IMR90	lung:	n/a	chr1:170512234-170512249
4	MAFK	chr1:170512212-170512382	HepG2	liver:	n/a	chr1:170512234-170512249

No.	Distal block	Cell Line	Cell type
1	chr1:170500119..170501652-chr1:170512143..170514479,2	MCF-7	breast:
2	chr1:170499494..170507345-chr1:170507805..170517333,18	K562	blood:
3	chr1:170499901..170503545-chr1:170509755..170513023,4	K562	blood:

Variant related genes	Relation type
GORAB	TF binding region
ENSG00000120370	Chromatin interaction
ENSG00000231407	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10733056	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10753814	0.91[AFR][1000 genomes]
rs10753815	0.92[ASW][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs10800527	1.00[ASW][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10919425	0.88[AFR][1000 genomes]
rs10919429	1.00[AMR][1000 genomes]
rs12068399	1.00[AMR][1000 genomes]
rs12116909	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs1333133	0.92[ASW][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs1333142	1.00[YRI][hapmap]
rs1333150	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1333155	0.90[AFR][1000 genomes]
rs1333156	0.90[AFR][1000 genomes]
rs1412892	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1412893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1412895	0.90[AFR][1000 genomes]
rs1537390	1.00[YRI][hapmap]
rs1537395	0.84[YRI][hapmap]
rs1537397	0.92[ASW][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs1576979	0.89[AFR][1000 genomes]
rs1576980	0.88[AFR][1000 genomes]
rs16863435	0.91[ASW][hapmap];1.00[AMR][1000 genomes]
rs1855221	0.90[AFR][1000 genomes]
rs1928716	1.00[YRI][hapmap]
rs1930632	0.81[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2104918	0.87[AFR][1000 genomes]
rs2150029	0.92[ASW][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2225322	0.92[ASW][hapmap];0.86[LWK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs2901401	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs3980839	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4233350	0.82[AFR][1000 genomes]
rs4325194	0.94[AFR][1000 genomes]
rs4402174	0.90[AFR][1000 genomes]
rs4415629	0.94[AFR][1000 genomes]
rs4656769	0.85[AFR][1000 genomes]
rs4656775	0.92[AFR][1000 genomes]
rs4656777	0.92[AFR][1000 genomes]
rs4656779	0.83[ASW][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs4656783	0.97[AFR][1000 genomes]
rs6427260	1.00[ASW][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6427261	1.00[ASW][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6657164	0.90[AFR][1000 genomes]
rs6660575	0.89[AFR][1000 genomes]
rs6664037	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6667304	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6669308	1.00[ASW][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6670724	0.88[AFR][1000 genomes]
rs6671312	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6676081	0.95[AFR][1000 genomes]
rs6693763	1.00[ASW][hapmap];0.97[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6699057	0.85[AFR][1000 genomes]
rs6701218	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6703801	0.82[AFR][1000 genomes]
rs7523665	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7531125	0.92[ASW][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs7538125	0.90[AFR][1000 genomes]
rs7548443	0.90[AFR][1000 genomes]
rs7553254	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170501800-170516000	Weak transcription	Spleen	Spleen
2	chr1:170502000-170515200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:170502000-170517200	Weak transcription	Esophagus	oesophagus
4	chr1:170502200-170521000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:170502400-170514800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:170502600-170520800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:170502600-170523400	Weak transcription	Fetal Brain Male	brain
8	chr1:170502800-170513800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:170503000-170513800	Weak transcription	Lung	lung
10	chr1:170503000-170513800	Weak transcription	Small Intestine	intestine
11	chr1:170503000-170516400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:170503000-170523600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:170503600-170512400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:170503800-170513400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:170503800-170516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:170504400-170514000	Weak transcription	K562	blood
17	chr1:170505000-170524800	Strong transcription	Dnd41	blood
18	chr1:170505400-170522800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:170506000-170522200	Strong transcription	Primary B cells from cord blood	blood
20	chr1:170506600-170513800	Weak transcription	Psoas Muscle	Psoas
21	chr1:170506600-170516800	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:170506600-170519200	Weak transcription	Gastric	stomach
23	chr1:170506600-170519200	Weak transcription	Right Ventricle	heart
24	chr1:170507200-170512600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:170507400-170513000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:170507400-170516400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:170507400-170516400	Weak transcription	HSMMtube	muscle
28	chr1:170507600-170515800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:170507600-170516200	Weak transcription	Stomach Mucosa	stomach
30	chr1:170507600-170523600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr1:170507600-170524000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:170507800-170516400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:170507800-170521800	Strong transcription	Fetal Lung	lung
34	chr1:170507800-170522200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:170507800-170522600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:170508000-170514600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:170508000-170516400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:170508000-170522000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:170508000-170523000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:170508200-170512600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:170508200-170512800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr1:170508200-170513600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:170508200-170513800	Strong transcription	NH-A	brain
44	chr1:170508200-170516400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:170508200-170522200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:170508200-170523400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:170508200-170524400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:170508400-170512600	Strong transcription	NHLF	lung
49	chr1:170508400-170512800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:170508400-170512800	Strong transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links