Variant report

Variant	rs325007
Chromosome Location	chr6:44269023-44269024
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	POLR2A	chr6:44269007-44269062	K562	blood:	n/a	n/a
2	POLR2A	chr6:44268739-44269140	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:44268896-44269272	K562	blood:	n/a	n/a
4	POLR2A	chr6:44268941-44269189	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
TCTE1	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11571907	1.00[ASN][1000 genomes]
rs11571915	1.00[ASN][1000 genomes]
rs11571917	1.00[ASN][1000 genomes]
rs11571951	1.00[ASN][1000 genomes]
rs11571957	1.00[ASN][1000 genomes]
rs11571998	1.00[ASN][1000 genomes]
rs11572002	1.00[ASN][1000 genomes]
rs11572056	1.00[ASN][1000 genomes]
rs12193699	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1293204	1.00[ASN][1000 genomes]
rs1331293	1.00[ASN][1000 genomes]
rs1411905	1.00[ASN][1000 genomes]
rs161706	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324136	0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324141	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs324143	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs325005	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325006	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325008	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325009	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325010	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs325011	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35260018	0.96[EUR][1000 genomes]
rs4308546	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4499913	0.86[AFR][1000 genomes]
rs4714775	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4714778	1.00[ASN][1000 genomes]
rs482336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484757	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs505617	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs511088	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs534416	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567192	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568902	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61462867	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650075	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651297	0.83[ASW][hapmap]
rs6927345	1.00[ASN][1000 genomes]
rs7740535	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs865027	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9357439	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9369483	1.00[ASN][1000 genomes]
rs9472241	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9472243	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472244	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
7	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
8	esv1807818	chr6:44266574-44275011	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 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	chr6:44265000-44269800	Weak transcription	Hela-S3	cervix
2	chr6:44265600-44279600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:44265800-44269400	Weak transcription	K562	blood
4	chr6:44265800-44270000	Weak transcription	HMEC	breast
5	chr6:44266000-44269800	Weak transcription	GM12878-XiMat	blood
6	chr6:44266000-44271600	Weak transcription	NHDF-Ad	bronchial
7	chr6:44266000-44272400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:44266000-44276600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:44266000-44277000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:44266000-44280000	Weak transcription	Small Intestine	intestine
11	chr6:44266200-44269600	Weak transcription	Fetal Lung	lung
12	chr6:44266200-44269800	Weak transcription	HSMMtube	muscle
13	chr6:44266200-44270000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:44266200-44270800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr6:44266200-44271200	Weak transcription	Fetal Brain Male	brain
16	chr6:44266200-44276400	Weak transcription	Fetal Heart	heart
17	chr6:44266200-44276800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:44266200-44279600	Weak transcription	Right Atrium	heart
19	chr6:44266400-44269800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:44266800-44269400	Weak transcription	HUVEC	blood vessel
21	chr6:44266800-44272400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:44266800-44273600	Strong transcription	Fetal Stomach	stomach
23	chr6:44266800-44276600	Strong transcription	Fetal Intestine Small	intestine
24	chr6:44266800-44279200	Strong transcription	Brain Cingulate Gyrus	brain
25	chr6:44266800-44279800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:44267000-44269400	Weak transcription	NH-A	brain
27	chr6:44267000-44269800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:44267000-44272800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:44267000-44275400	Weak transcription	Fetal Kidney	kidney
30	chr6:44267000-44276600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:44267000-44279600	Strong transcription	Fetal Muscle Leg	muscle
32	chr6:44267000-44279800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:44267000-44279800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr6:44267200-44279400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:44267200-44279600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:44267200-44279600	Strong transcription	Fetal Thymus	thymus
37	chr6:44267200-44279800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:44267200-44279800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:44267400-44270200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr6:44267400-44272800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:44267400-44275400	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:44267400-44275600	Strong transcription	NHLF	lung
43	chr6:44267400-44276400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:44267400-44276600	Strong transcription	NHEK	skin
45	chr6:44267400-44276800	Strong transcription	Fetal Intestine Large	intestine
46	chr6:44267400-44279200	Strong transcription	Liver	Liver
47	chr6:44267400-44279400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:44267400-44279600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:44267400-44279600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:44267400-44280000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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