Variant report

Variant	rs6692369
Chromosome Location	chr1:78005179-78005180
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	TCF12	chr1:78004391-78006017	SK-N-SH	brain:	n/a	n/a
2	STAT1	chr1:78004728-78006805	Hela-S3	cervix:	n/a	chr1:78006375-78006384
3	MAX	chr1:78004568-78005543	A549	lung:	n/a	n/a
4	FOXA2	chr1:78004633-78005328	HepG2	liver:	n/a	n/a
5	FOSL2	chr1:78004536-78006029	SK-N-SH	brain:	n/a	chr1:78005610-78005619
6	POLR2A	chr1:78004473-78006648	U87	brain:	n/a	n/a
7	SMARCC1	chr1:78004743-78006663	Hela-S3	cervix:	n/a	n/a
8	MAFK	chr1:78004790-78005879	IMR90	lung:	n/a	chr1:78005622-78005631 chr1:78005615-78005635 chr1:78005621-78005631 chr1:78005617-78005633
9	MAX	chr1:78004792-78005884	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr1:78004364-78006643	A549	lung:	n/a	n/a
11	NFIC	chr1:78004540-78006037	SK-N-SH	brain:	n/a	n/a
12	MAX	chr1:78004395-78006031	A549	lung:	n/a	n/a
13	YY1	chr1:78004646-78005851	SK-N-SH	brain:	n/a	n/a
14	FOS	chr1:78004908-78005188	MCF10A-Er-Src	breast:	n/a	n/a
15	TFAP2C	chr1:78005012-78006925	Hela-S3	cervix:	n/a	n/a
16	PBX3	chr1:78004498-78006058	SK-N-SH	brain:	n/a	n/a
17	JUND	chr1:78004698-78006012	SK-N-SH	brain:	n/a	chr1:78005610-78005619
18	EP300	chr1:78004662-78006119	SK-N-SH	brain:	n/a	chr1:78005869-78005882
19	GATA3	chr1:78004360-78006650	A549	lung:	n/a	n/a
20	SP1	chr1:78004491-78006024	A549	lung:	n/a	chr1:78005493-78005507 chr1:78005328-78005337
21	POLR2A	chr1:78004854-78005292	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr1:78004532-78006692	U87	brain:	n/a	n/a
23	CEBPB	chr1:78004592-78006983	Hela-S3	cervix:	n/a	n/a
24	GATA3	chr1:78004581-78005999	SK-N-SH	brain:	n/a	n/a
25	PBX3	chr1:78004622-78006044	SK-N-SH	brain:	n/a	n/a
26	EP300	chr1:78004502-78005845	A549	lung:	n/a	n/a
27	POLR2A	chr1:78004704-78005917	SK-N-SH	brain:	n/a	n/a
28	CEBPB	chr1:78004548-78005230	IMR90	lung:	n/a	n/a
29	GATA3	chr1:78004480-78006099	SK-N-SH	brain:	n/a	n/a
30	MAX	chr1:78004457-78005934	A549	lung:	n/a	n/a
31	TCF12	chr1:78004404-78006421	SK-N-SH	brain:	n/a	n/a
32	CTCF	chr1:78005060-78005210	HBMEC	blood vessel:	n/a	n/a
33	RCOR1	chr1:78004955-78006618	Hela-S3	cervix:	n/a	n/a
34	FOS	chr1:78004855-78005194	MCF10A-Er-Src	breast:	n/a	n/a
35	MAX	chr1:78004619-78005348	SK-N-SH	brain:	n/a	n/a
36	EP300	chr1:78004502-78005957	A549	lung:	n/a	chr1:78005869-78005882
37	FOXA2	chr1:78004516-78005214	A549	lung:	n/a	n/a
38	FOS	chr1:78004861-78005193	MCF10A-Er-Src	breast:	n/a	n/a
39	FOSL2	chr1:78004905-78005229	A549	lung:	n/a	n/a
40	RXRA	chr1:78004721-78006071	SK-N-SH	brain:	n/a	n/a
41	CEBPB	chr1:78004498-78005306	A549	lung:	n/a	n/a
42	SIN3AK20	chr1:78004976-78005450	SK-N-SH	brain:	n/a	n/a
43	FOS	chr1:78004845-78005203	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr1:78005099-78005190	A549	lung:	n/a	n/a
45	REST	chr1:78004539-78005203	A549	lung:	n/a	n/a
46	FOXA2	chr1:78004489-78005199	A549	lung:	n/a	n/a
47	POLR2A	chr1:78004477-78006805	U87	brain:	n/a	n/a
48	CEBPB	chr1:78004667-78005222	A549	lung:	n/a	n/a
49	POLR2A	chr1:78005080-78005471	ProgFib	skin:	n/a	n/a
50	FOSL2	chr1:78004438-78005999	A549	lung:	n/a	chr1:78005610-78005619

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77999652..78002822-chr1:78004325..78005902,3	K562	blood:

Variant related genes	Relation type
AK5	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1013399	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10782654	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873949	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10873950	0.96[ASN][1000 genomes]
rs10873951	0.84[ASN][1000 genomes]
rs11162362	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11162363	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11162364	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162365	0.92[ASN][1000 genomes]
rs11162369	0.85[ASN][1000 genomes]
rs11162372	0.83[ASN][1000 genomes]
rs12071212	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12074409	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12095064	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12717767	0.92[ASN][1000 genomes]
rs12724560	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565850	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1565851	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1565852	0.88[ASN][1000 genomes]
rs1962523	0.92[ASN][1000 genomes]
rs1976334	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2029768	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2133202	0.88[ASN][1000 genomes]
rs2172727	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2647486	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2647487	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278862	0.81[ASN][1000 genomes]
rs2803136	0.95[ASN][1000 genomes]
rs2803168	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34773766	0.91[ASN][1000 genomes]
rs3509	0.96[ASN][1000 genomes]
rs371076	0.81[ASN][1000 genomes]
rs3738079	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767032	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767033	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4245658	0.97[ASN][1000 genomes]
rs4589153	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4600093	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4949657	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949658	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4949659	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4949807	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949808	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4949809	0.97[ASN][1000 genomes]
rs4949811	0.94[ASN][1000 genomes]
rs4949813	0.93[ASN][1000 genomes]
rs4949816	0.88[ASN][1000 genomes]
rs6603952	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6603953	0.93[ASN][1000 genomes]
rs6603955	0.92[ASN][1000 genomes]
rs6667519	0.97[ASN][1000 genomes]
rs6667803	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6675743	0.97[ASN][1000 genomes]
rs6695989	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696083	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs728741	0.93[ASN][1000 genomes]
rs7513619	0.84[ASN][1000 genomes]
rs7519476	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7524147	0.97[ASN][1000 genomes]
rs7524866	0.97[ASN][1000 genomes]
rs7531286	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7545544	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7551211	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7551729	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs962388	0.93[ASN][1000 genomes]
rs9787153	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871143	chr1:77955577-78031994	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1533	chr1:77990504-78036279	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77983000-78009200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:77998000-78014000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:77999600-78009600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:77999800-78005200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:78000000-78011600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:78000000-78030600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:78000000-78031200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:78000800-78006800	Strong transcription	Primary T cells from cord blood	blood
9	chr1:78001400-78006600	Enhancers	NHEK	skin
10	chr1:78001600-78005800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:78001600-78006200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:78001600-78006600	Enhancers	HMEC	breast
13	chr1:78001800-78006600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:78002200-78005200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:78003600-78005600	Enhancers	Liver	Liver
16	chr1:78003800-78006000	Enhancers	Fetal Muscle Leg	muscle
17	chr1:78004000-78005200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:78004200-78007800	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:78004400-78005400	Enhancers	Fetal Kidney	kidney
20	chr1:78004400-78006000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:78004400-78006200	Enhancers	Stomach Mucosa	stomach
22	chr1:78004400-78006200	Flanking Active TSS	A549	lung
23	chr1:78004400-78006400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:78004400-78007600	Enhancers	GM12878-XiMat	blood
25	chr1:78004600-78005800	Enhancers	Brain Angular Gyrus	brain
26	chr1:78004600-78005800	Enhancers	Fetal Muscle Trunk	muscle
27	chr1:78004600-78006000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:78004600-78006000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr1:78004600-78006000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:78004600-78006000	Enhancers	Brain Substantia Nigra	brain
31	chr1:78004600-78006000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr1:78004600-78006000	Flanking Active TSS	NH-A	brain
33	chr1:78004600-78006200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:78004600-78006200	Enhancers	Brain Cingulate Gyrus	brain
35	chr1:78004600-78006200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr1:78004600-78006400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:78004600-78006600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr1:78004600-78006600	Flanking Active TSS	Osteobl	bone
39	chr1:78004600-78008200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:78004800-78005400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:78004800-78005400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr1:78004800-78005400	Flanking Active TSS	HepG2	liver
43	chr1:78004800-78005600	Enhancers	Fetal Heart	heart
44	chr1:78004800-78005600	Enhancers	Fetal Stomach	stomach
45	chr1:78004800-78005800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:78004800-78005800	Enhancers	Psoas Muscle	Psoas
47	chr1:78004800-78006200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:78004800-78006200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:78004800-78006200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:78004800-78006400	Flanking Active TSS	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links