Variant report

Variant	rs9350803
Chromosome Location	chr6:79942876-79942877
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	POLR2A	chr6:79942836-79944809	GM12891	blood:	n/a	n/a
2	SETDB1	chr6:79942569-79943679	U2OS	brain:	n/a	n/a
3	WRNIP1	chr6:79942820-79942998	GM12878	blood:	n/a	n/a
4	STAT3	chr6:79942803-79943497	MCF10A-Er-Src	breast:	n/a	chr6:79943330-79943342
5	POLR2A	chr6:79942550-79944754	GM12878	blood:	n/a	n/a
6	RFX5	chr6:79942075-79945226	SK-N-SH	brain:	n/a	chr6:79944581-79944596
7	KAP1	chr6:79942796-79945275	U2OS	brain:	n/a	chr6:79943761-79943769

No.	Distal block	Cell Line	Cell type
1	chr6:79785425..79789135-chr6:79942833..79950296,12	MCF-7	breast:
2	chr6:79782683..79789958-chr6:79939846..79945776,22	MCF-7	breast:
3	chr6:79763581..79765481-chr6:79941505..79943028,2	K562	blood:
4	chr6:79785468..79790645-chr6:79941426..79946271,8	K562	blood:

Variant related genes	Relation type
HMGN3-AS1	TF binding region
ENSG00000146247	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10455359	0.94[EUR][1000 genomes]
rs10806163	0.91[EUR][1000 genomes]
rs11965180	0.92[EUR][1000 genomes]
rs11966786	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11969279	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12194892	0.91[EUR][1000 genomes]
rs12209677	0.91[EUR][1000 genomes]
rs1335535	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1335537	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[EUR][1000 genomes]
rs1335538	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[EUR][1000 genomes]
rs1414279	0.91[EUR][1000 genomes]
rs1414283	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1414284	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1537739	0.92[EUR][1000 genomes]
rs1537740	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1582079	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16890450	0.91[EUR][1000 genomes]
rs16890704	1.00[MEX][hapmap]
rs1832088	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1832089	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1889685	0.92[EUR][1000 genomes]
rs2095633	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2322216	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2322219	0.92[EUR][1000 genomes]
rs2874732	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2874733	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3934335	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4112504	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4235810	0.92[EUR][1000 genomes]
rs4301272	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4377755	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4407672	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4418150	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs4432946	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4464749	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4470813	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4537102	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4555887	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4706754	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4706755	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4706756	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4706759	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4706760	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4706765	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[EUR][1000 genomes]
rs4706766	0.94[EUR][1000 genomes]
rs55635444	0.94[EUR][1000 genomes]
rs56183421	0.92[EUR][1000 genomes]
rs56193084	0.91[EUR][1000 genomes]
rs56354335	0.91[EUR][1000 genomes]
rs56955811	0.91[EUR][1000 genomes]
rs57340384	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57608966	0.91[EUR][1000 genomes]
rs59152048	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs59858042	0.94[EUR][1000 genomes]
rs61227507	0.94[EUR][1000 genomes]
rs61558200	0.91[EUR][1000 genomes]
rs62411290	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6454106	0.94[EUR][1000 genomes]
rs6907042	0.94[EUR][1000 genomes]
rs6907264	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6913297	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6917165	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6924790	0.94[EUR][1000 genomes]
rs6929660	0.92[EUR][1000 genomes]
rs6941433	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73468020	0.94[EUR][1000 genomes]
rs73468035	0.91[EUR][1000 genomes]
rs73767530	0.91[EUR][1000 genomes]
rs7738508	0.94[EUR][1000 genomes]
rs7739118	0.92[EUR][1000 genomes]
rs7746915	0.94[EUR][1000 genomes]
rs7751974	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7752593	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7757062	0.92[EUR][1000 genomes]
rs7760458	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7760939	0.92[EUR][1000 genomes]
rs7763232	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7764517	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7770245	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7772967	0.94[EUR][1000 genomes]
rs9343886	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9343890	0.89[EUR][1000 genomes]
rs9352710	0.94[EUR][1000 genomes]
rs9359369	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9361504	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9361511	0.94[EUR][1000 genomes]
rs9443654	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs989191	0.82[LWK][hapmap];0.84[YRI][hapmap]

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	nsv830706	chr6:79825910-79994878	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79913200-79943000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:79913200-79943200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:79916400-79943200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:79920400-79943000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:79936200-79943000	Weak transcription	Fetal Intestine Large	intestine
6	chr6:79936200-79943000	Weak transcription	Psoas Muscle	Psoas
7	chr6:79936200-79943200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:79940800-79943000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr6:79941000-79943000	Enhancers	Fetal Heart	heart
10	chr6:79941200-79943200	Weak transcription	Pancreas	Pancrea
11	chr6:79941600-79943000	Enhancers	Fetal Intestine Small	intestine
12	chr6:79941600-79943000	Enhancers	Placenta	Placenta
13	chr6:79941600-79945000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr6:79941800-79943000	Enhancers	Brain Angular Gyrus	brain
15	chr6:79941800-79943200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:79942000-79943000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:79942000-79943000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:79942000-79943000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:79942000-79943000	Enhancers	Brain Substantia Nigra	brain
20	chr6:79942000-79943000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr6:79942000-79943200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:79942000-79943200	Enhancers	Gastric	stomach
23	chr6:79942000-79943200	Enhancers	Ovary	ovary
24	chr6:79942000-79943200	Flanking Active TSS	Dnd41	blood
25	chr6:79942200-79943000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:79942200-79943200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:79942200-79943200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr6:79942200-79943200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:79942200-79943200	Weak transcription	Esophagus	oesophagus
30	chr6:79942200-79943200	Enhancers	Fetal Brain Male	brain
31	chr6:79942200-79943200	Enhancers	Small Intestine	intestine
32	chr6:79942200-79944800	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr6:79942400-79943000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr6:79942400-79943000	Enhancers	Primary B cells from cord blood	blood
35	chr6:79942400-79943000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:79942400-79943000	Weak transcription	K562	blood
37	chr6:79942400-79944800	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr6:79942400-79944800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:79942400-79944800	Active TSS	GM12878-XiMat	blood
40	chr6:79942600-79943000	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr6:79942600-79943000	Enhancers	Primary T cells fromperipheralblood	blood
42	chr6:79942600-79943000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr6:79942600-79943000	Flanking Active TSS	Fetal Thymus	thymus
44	chr6:79942600-79943000	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr6:79942600-79943200	Enhancers	Primary B cells from peripheral blood	blood
46	chr6:79942600-79944200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:79942600-79944800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:79942600-79944800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:79942600-79944800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:79942800-79943000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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