Variant report

Variant	rs2270888
Chromosome Location	chr9:2811505-2811506
allele	A/C/G/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	chr9:2811282-2811506	GM12878	blood:	n/a	n/a
2	POLR2A	chr9:2811227-2811594	HL-60	blood:	n/a	n/a
3	POLR2A	chr9:2811153-2811585	GM12892	blood:	n/a	n/a
4	POLR2A	chr9:2810470-2812135	A549	lung:	n/a	n/a
5	POLR2A	chr9:2810517-2811736	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:2811240-2811639	GM12891	blood:	n/a	n/a
7	POLR2A	chr9:2811262-2811607	GM12892	blood:	n/a	n/a
8	CTCF	chr9:2811460-2811610	GM12869	blood:	n/a	n/a
9	POLR2A	chr9:2810680-2811533	GM12891	blood:	n/a	n/a
10	POLR2A	chr9:2809393-2812119	HepG2	liver:	n/a	n/a
11	POLR2A	chr9:2809776-2811903	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr9:2811213-2811644	GM12891	blood:	n/a	n/a
13	POLR2A	chr9:2810412-2811669	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:2776529..2778337-chr9:2809907..2812711,2	K562	blood:
2	chr9:2808764..2811961-chr9:2812459..2815898,4	K562	blood:
3	chr9:2257367..2260216-chr9:2810940..2813820,2	MCF-7	breast:

Variant related genes	Relation type
KIAA0020	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10481516	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10738791	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10757715	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10812719	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10968361	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3739460	0.84[CHB][hapmap]
rs4439183	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs6476038	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv892079	chr9:2681430-2931341	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv892081	chr9:2691186-2851026	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv892082	chr9:2699606-2833267	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv1024262	chr9:2703159-3067931	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1028011	chr9:2759097-2904277	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	nsv1022873	chr9:2768825-2863264	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv892083	chr9:2809548-2900651	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2787800-2812200	Strong transcription	Fetal Muscle Trunk	muscle
2	chr9:2791600-2815800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:2791800-2821800	Strong transcription	Primary T cells from cord blood	blood
4	chr9:2792000-2822200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr9:2792200-2813000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:2793200-2826600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:2793400-2814200	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr9:2794400-2814800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:2795200-2817600	Weak transcription	Stomach Mucosa	stomach
10	chr9:2795400-2814000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr9:2796400-2822200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr9:2796600-2813200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr9:2796800-2812600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr9:2797600-2813400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr9:2797600-2813600	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr9:2797800-2813000	Strong transcription	Dnd41	blood
17	chr9:2797800-2813800	Strong transcription	Primary B cells from cord blood	blood
18	chr9:2797800-2813800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr9:2798000-2837400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:2798400-2812600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr9:2798800-2811600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr9:2800200-2812000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:2801200-2812200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr9:2801200-2813800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:2801200-2838600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:2801400-2813800	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr9:2801600-2837200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:2801800-2814200	Strong transcription	HMEC	breast
29	chr9:2802400-2814200	Strong transcription	GM12878-XiMat	blood
30	chr9:2803200-2814000	Strong transcription	NHEK	skin
31	chr9:2803600-2812000	Strong transcription	HUVEC	blood vessel
32	chr9:2803600-2829200	Weak transcription	Small Intestine	intestine
33	chr9:2804400-2813800	Strong transcription	K562	blood
34	chr9:2805800-2829400	Weak transcription	Fetal Brain Male	brain
35	chr9:2807000-2812000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr9:2807000-2812200	Strong transcription	Fetal Thymus	thymus
37	chr9:2807400-2811600	Strong transcription	Fetal Brain Female	brain
38	chr9:2807600-2811600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:2807800-2812200	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr9:2808200-2811600	Strong transcription	Brain Hippocampus Middle	brain
41	chr9:2808200-2811600	Genic enhancers	Osteobl	bone
42	chr9:2808200-2812400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr9:2808400-2814000	Strong transcription	Primary hematopoietic stem cells	blood
44	chr9:2808400-2814000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:2808400-2814000	Enhancers	Fetal Heart	heart
46	chr9:2808600-2811600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:2808600-2811600	Strong transcription	Brain Anterior Caudate	brain
48	chr9:2808600-2811600	Genic enhancers	Fetal Stomach	stomach
49	chr9:2808600-2811600	Genic enhancers	HSMM	muscle
50	chr9:2808600-2812200	Strong transcription	Lung	lung

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