Variant report

Variant	rs9405694
Chromosome Location	chr6:4024514-4024515
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	IRF1	chr6:4023506-4024527	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:4016355..4024618-chr6:4131840..4138381,21	K562	blood:
2	chr6:4017302..4025509-chr6:4131840..4138381,19	K562	blood:
3	chr6:4017127..4021712-chr6:4024142..4029441,9	MCF-7	breast:
4	chr6:3161756..3164171-chr6:4023037..4024626,2	K562	blood:
5	chr6:3354766..3356285-chr6:4022348..4024808,2	K562	blood:

Variant related genes	Relation type
ENSG00000230648	TF binding region
ENSG00000112739	Chromatin interaction
ENSG00000254821	Chromatin interaction
ENSG00000230648	Chromatin interaction
ENSG00000272248	Chromatin interaction
ENSG00000198721	Chromatin interaction
ENSG00000234817	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12174184	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408457	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543355	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1969837	0.83[EUR][1000 genomes]
rs2181894	0.95[ASN][1000 genomes]
rs2745451	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2745452	0.81[EUR][1000 genomes]
rs3747761	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747762	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747763	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761787	0.98[ASN][1000 genomes]
rs4466281	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959916	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959918	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4959919	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6900476	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905475	0.83[ASN][1000 genomes]
rs6906467	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910519	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914180	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916982	0.95[ASN][1000 genomes]
rs6921738	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6930892	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933593	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6941706	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs697745	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707980	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707981	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707982	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707983	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707984	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707985	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707987	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs707988	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73349780	0.84[ASN][1000 genomes]
rs7744603	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7763233	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853396	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs853397	0.93[ASN][1000 genomes]
rs853398	0.94[ASN][1000 genomes]
rs853399	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853400	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853402	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853403	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853404	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853405	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853406	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853407	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853408	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853409	0.81[ASN][1000 genomes]
rs853410	0.83[ASN][1000 genomes]
rs853411	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs860477	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860478	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9328215	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328216	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9392546	0.81[EUR][1000 genomes]
rs9405217	0.81[EUR][1000 genomes]
rs941443	0.95[ASN][1000 genomes]
rs942474	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9503893	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 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	chr6:4021000-4025000	Active TSS	GM12878-XiMat	blood
2	chr6:4021000-4025200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr6:4022400-4025600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:4022400-4028400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:4022400-4043400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:4022600-4049400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:4022800-4024600	Enhancers	Small Intestine	intestine
8	chr6:4023000-4024600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:4023000-4025800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr6:4023000-4027000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr6:4023000-4027000	Weak transcription	Left Ventricle	heart
12	chr6:4023000-4028400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:4023000-4028400	Weak transcription	Ovary	ovary
14	chr6:4023000-4032000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:4023000-4038600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:4023000-4063600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:4023200-4024600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr6:4023200-4024600	Enhancers	Fetal Muscle Leg	muscle
19	chr6:4023200-4024600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr6:4023200-4025800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr6:4023200-4027600	Weak transcription	Brain Angular Gyrus	brain
22	chr6:4023200-4028400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:4023200-4031800	Weak transcription	Placenta	Placenta
24	chr6:4023200-4034000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr6:4023200-4035600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:4023200-4043400	Weak transcription	Aorta	Aorta
27	chr6:4023200-4064000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:4023400-4024600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:4023400-4024600	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr6:4023400-4024600	Enhancers	Duodenum Mucosa	Duodenum
31	chr6:4023400-4024600	Enhancers	Fetal Intestine Large	intestine
32	chr6:4023400-4024800	Enhancers	Rectal Smooth Muscle	rectum
33	chr6:4023400-4025000	Enhancers	Primary hematopoietic stem cells	blood
34	chr6:4023400-4025200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:4023400-4025200	Enhancers	Liver	Liver
36	chr6:4023400-4025600	Weak transcription	Brain Anterior Caudate	brain
37	chr6:4023400-4026000	Enhancers	Adipose Nuclei	Adipose
38	chr6:4023400-4026400	Enhancers	Colon Smooth Muscle	Colon
39	chr6:4023400-4027000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:4023400-4027600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr6:4023400-4029200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:4023400-4038800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:4023400-4040600	Weak transcription	Fetal Brain Male	brain
44	chr6:4023400-4071600	Weak transcription	Stomach Mucosa	stomach
45	chr6:4023600-4024600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:4023600-4024600	Genic enhancers	Fetal Thymus	thymus
47	chr6:4023600-4024800	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr6:4023600-4025000	Enhancers	Pancreas	Pancrea
49	chr6:4023600-4025400	Weak transcription	Brain Germinal Matrix	brain
50	chr6:4023600-4026000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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