Variant report

Variant	rs6669308
Chromosome Location	chr1:170505617-170505618
allele	A/G
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	BACH1	chr1:170505483-170505643	K562	blood:	n/a	n/a
2	POLR2A	chr1:170500588-170509342	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:170499484..170505100-chr1:170505427..170511134,13	MCF-7	breast:
2	chr1:170505266..170507420-chr1:170507525..170509376,2	K562	blood:
3	chr1:170499494..170507345-chr1:170507805..170517333,18	K562	blood:
4	chr1:170500034..170503040-chr1:170504550..170507151,5	K562	blood:

Variant related genes	Relation type
GORAB	TF binding region
ENSG00000231407	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];0.89[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs10800527	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];0.91[LWK][hapmap];0.96[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];0.89[LWK][hapmap];0.96[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[MEX][hapmap];1.00[AMR][1000 genomes]
rs1855221	0.90[AFR][1000 genomes]
rs1928716	1.00[YRI][hapmap]
rs1930632	0.85[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2104918	0.87[AFR][1000 genomes]
rs2150029	0.92[ASW][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2225322	0.92[ASW][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs2421325	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]
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];0.88[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs4656783	0.97[AFR][1000 genomes]
rs6427260	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6427261	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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]
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];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[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];0.89[LWK][hapmap];0.96[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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170501800-170516000	Weak transcription	Spleen	Spleen
2	chr1:170502000-170506200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:170502000-170506200	Weak transcription	Gastric	stomach
4	chr1:170502000-170508400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:170502000-170515200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:170502000-170517200	Weak transcription	Esophagus	oesophagus
7	chr1:170502200-170508200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:170502200-170508400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:170502200-170508400	Weak transcription	Placenta	Placenta
10	chr1:170502200-170508400	Weak transcription	Fetal Thymus	thymus
11	chr1:170502200-170508400	Weak transcription	Thymus	Thymus
12	chr1:170502200-170521000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:170502400-170506400	Weak transcription	Right Atrium	heart
14	chr1:170502400-170512200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:170502400-170514800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:170502600-170507200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:170502600-170507800	Weak transcription	Fetal Lung	lung
18	chr1:170502600-170508400	Weak transcription	Fetal Intestine Small	intestine
19	chr1:170502600-170508600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:170502600-170508600	Weak transcription	Fetal Brain Female	brain
21	chr1:170502600-170509000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:170502600-170509800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:170502600-170510200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:170502600-170510200	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:170502600-170511600	Weak transcription	Brain Substantia Nigra	brain
26	chr1:170502600-170512000	Weak transcription	Aorta	Aorta
27	chr1:170502600-170520800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:170502600-170523400	Weak transcription	Fetal Brain Male	brain
29	chr1:170502800-170506000	Weak transcription	Stomach Mucosa	stomach
30	chr1:170502800-170506400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:170502800-170506400	Weak transcription	Psoas Muscle	Psoas
32	chr1:170502800-170506400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:170502800-170506800	Weak transcription	A549	lung
34	chr1:170502800-170507200	Weak transcription	HUVEC	blood vessel
35	chr1:170502800-170507600	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr1:170502800-170507800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:170502800-170508200	Weak transcription	Fetal Stomach	stomach
38	chr1:170502800-170508400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:170502800-170508400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:170502800-170508400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr1:170502800-170508400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:170502800-170508400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:170502800-170508400	Weak transcription	Fetal Intestine Large	intestine
44	chr1:170502800-170508800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:170502800-170509600	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:170502800-170509600	Weak transcription	Brain Germinal Matrix	brain
47	chr1:170502800-170509800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:170502800-170512200	Weak transcription	Brain Anterior Caudate	brain
49	chr1:170502800-170513800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:170503000-170506200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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