Variant report

Variant	rs12341021
Chromosome Location	chr9:6009656-6009657
allele	C/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	chr9:6009433-6010061	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr9:6009630-6009926	GM12891	blood:	n/a	n/a
3	POLR2A	chr9:6009572-6009839	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:6008201-6010366	K562	blood:	n/a	n/a
5	POLR2A	chr9:6009594-6009688	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:6006778..6010531-chr9:6011866..6018012,11	MCF-7	breast:
2	chr9:5832476..5834522-chr9:6008226..6010221,2	MCF-7	breast:
3	chr9:5982537..5984417-chr9:6009153..6011751,2	K562	blood:

Variant related genes	Relation type
KIAA2026	TF binding region
ENSG00000099219	Chromatin interaction
ENSG00000137040	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10116214	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124484	1.00[CHB][hapmap]
rs10125832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10975377	0.95[YRI][hapmap];0.84[AFR][1000 genomes];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	1.00[CHB][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339713	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339886	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339889	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340153	1.00[EUR][1000 genomes]
rs12340531	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342166	1.00[EUR][1000 genomes]
rs12342282	0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12343325	1.00[EUR][1000 genomes]
rs12345849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351533	1.00[EUR][1000 genomes]
rs12352918	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1330124	1.00[CHB][hapmap]
rs1411949	1.00[EUR][1000 genomes]
rs1993912	1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28431078	1.00[EUR][1000 genomes]
rs28706504	1.00[EUR][1000 genomes]
rs380568	1.00[CHB][hapmap]
rs386775	1.00[EUR][1000 genomes]
rs57154492	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58291302	0.82[AFR][1000 genomes];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	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383113	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383114	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383144	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73385128	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73387085	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73389036	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389044	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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853706	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7854980	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7858084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859471	1.00[CHB][hapmap]
rs7875607	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

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	chr9:6009000-6009800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:6009000-6009800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:6009000-6010000	Enhancers	Hela-S3	cervix
18	chr9:6009000-6010000	Enhancers	HepG2	liver
19	chr9:6009000-6011400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr9:6009000-6011600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:6009000-6012400	Weak transcription	Placenta	Placenta
22	chr9:6009000-6012400	Weak transcription	Right Ventricle	heart
23	chr9:6009000-6012600	Weak transcription	Fetal Muscle Leg	muscle
24	chr9:6009000-6012800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:6009000-6013600	Weak transcription	Aorta	Aorta
26	chr9:6009000-6013800	Weak transcription	Fetal Stomach	stomach
27	chr9:6009000-6014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:6009000-6014200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:6009000-6014400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:6009000-6014400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:6009000-6014400	Weak transcription	Ovary	ovary
32	chr9:6009000-6014600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:6009200-6009800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr9:6009200-6009800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:6009200-6009800	Enhancers	Fetal Heart	heart
36	chr9:6009200-6009800	Enhancers	NHEK	skin
37	chr9:6009200-6010000	Enhancers	Primary hematopoietic stem cells	blood
38	chr9:6009200-6010000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr9:6009200-6010000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr9:6009200-6011000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:6009200-6011000	Weak transcription	Primary T cells from cord blood	blood
42	chr9:6009200-6011400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:6009200-6011400	Weak transcription	Fetal Thymus	thymus
44	chr9:6009200-6011400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr9:6009200-6011600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr9:6009200-6011600	Weak transcription	Brain Angular Gyrus	brain
47	chr9:6009200-6011600	Weak transcription	Fetal Brain Female	brain
48	chr9:6009200-6011800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:6009200-6011800	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr9:6009200-6011800	Weak transcription	Adipose Nuclei	Adipose

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