Variant report

Variant	rs73389044
Chromosome Location	chr9:6011252-6011253
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	chr9:6011071-6011485	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:5975596..5977184-chr9:6010067..6012424,2	K562	blood:
2	chr9:5982537..5984417-chr9:6009153..6011751,2	K562	blood:

Variant related genes	Relation type
KIAA2026	TF binding region

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

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10116214	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10125832	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10975350	1.00[EUR][1000 genomes]
rs10975351	1.00[EUR][1000 genomes]
rs10975362	1.00[EUR][1000 genomes]
rs10975363	1.00[EUR][1000 genomes]
rs10975364	1.00[EUR][1000 genomes]
rs10975372	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10975377	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11506678	1.00[EUR][1000 genomes]
rs11793956	0.91[AMR][1000 genomes]
rs12337300	1.00[EUR][1000 genomes]
rs12337445	1.00[EUR][1000 genomes]
rs12337790	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339713	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339886	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12340153	1.00[EUR][1000 genomes]
rs12340531	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12341021	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12342166	1.00[EUR][1000 genomes]
rs12342282	1.00[EUR][1000 genomes]
rs12343325	1.00[EUR][1000 genomes]
rs12345849	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12351533	1.00[EUR][1000 genomes]
rs12352918	0.83[AMR][1000 genomes]
rs1411949	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1993912	0.91[AMR][1000 genomes]
rs28431078	1.00[EUR][1000 genomes]
rs28706504	1.00[EUR][1000 genomes]
rs386775	1.00[EUR][1000 genomes]
rs57154492	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58291302	1.00[EUR][1000 genomes]
rs60037728	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7022080	1.00[EUR][1000 genomes]
rs7029847	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383109	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383113	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383114	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383144	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73385128	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73387085	0.83[AMR][1000 genomes]
rs73389036	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73397307	1.00[EUR][1000 genomes]
rs73397376	1.00[EUR][1000 genomes]
rs73399307	1.00[EUR][1000 genomes]
rs73639554	1.00[EUR][1000 genomes]
rs73639568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853706	0.91[AMR][1000 genomes]
rs7854980	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7858084	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7858846	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7875607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9299025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv824832	chr9:6010950-6014233	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv824833	chr9:6011129-6014118	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
9	nsv824834	chr9:6011129-6014233	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv824835	chr9:6011129-6014339	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6008000-6014800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:6008400-6013400	Weak transcription	Gastric	stomach
3	chr9:6008400-6014200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:6008600-6013800	Weak transcription	Small Intestine	intestine
5	chr9:6008600-6014400	Weak transcription	Esophagus	oesophagus
6	chr9:6008600-6015200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:6008800-6012400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:6008800-6012600	Weak transcription	Left Ventricle	heart
9	chr9:6008800-6013400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:6008800-6014200	Weak transcription	Lung	lung
11	chr9:6008800-6014400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:6008800-6014400	Weak transcription	Colonic Mucosa	Colon
13	chr9:6008800-6014400	Weak transcription	Spleen	Spleen
14	chr9:6008800-6014600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:6009000-6011400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr9:6009000-6011600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:6009000-6012400	Weak transcription	Placenta	Placenta
18	chr9:6009000-6012400	Weak transcription	Right Ventricle	heart
19	chr9:6009000-6012600	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:6009000-6012800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:6009000-6013600	Weak transcription	Aorta	Aorta
22	chr9:6009000-6013800	Weak transcription	Fetal Stomach	stomach
23	chr9:6009000-6014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr9:6009000-6014200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:6009000-6014400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:6009000-6014400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:6009000-6014400	Weak transcription	Ovary	ovary
28	chr9:6009000-6014600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:6009200-6011400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:6009200-6011400	Weak transcription	Fetal Thymus	thymus
31	chr9:6009200-6011400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr9:6009200-6011600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr9:6009200-6011600	Weak transcription	Brain Angular Gyrus	brain
34	chr9:6009200-6011600	Weak transcription	Fetal Brain Female	brain
35	chr9:6009200-6011800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:6009200-6011800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr9:6009200-6011800	Weak transcription	Adipose Nuclei	Adipose
38	chr9:6009200-6011800	Weak transcription	Brain Germinal Matrix	brain
39	chr9:6009200-6012000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr9:6009200-6012000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr9:6009200-6012200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:6009200-6012400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:6009200-6012400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr9:6009200-6012400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr9:6009200-6012400	Weak transcription	Fetal Kidney	kidney
46	chr9:6009200-6012600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr9:6009200-6012600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr9:6009200-6012800	Weak transcription	Psoas Muscle	Psoas
49	chr9:6009200-6012800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr9:6009200-6012800	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links