Variant report

Variant	rs4520217
Chromosome Location	chr9:2770887-2770888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2767181..2768946-chr9:2770729..2772819,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNV2-4	chr9:2770480-2771317	NONHSAT130009

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1060812	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10738777	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10738778	0.89[ASN][1000 genomes]
rs10738782	0.84[ASN][1000 genomes]
rs10757675	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10812639	0.83[EUR][1000 genomes]
rs1454635	0.80[EUR][1000 genomes]
rs1551410	0.88[ASN][1000 genomes]
rs2168134	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2168135	0.85[EUR][1000 genomes]
rs4623490	0.82[EUR][1000 genomes]
rs4740699	0.85[EUR][1000 genomes]
rs4741767	0.84[EUR][1000 genomes]
rs7027337	0.85[EUR][1000 genomes]
rs7035082	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7849358	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7869344	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs958505	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv531565	chr9:2682523-2784028	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv516425	chr9:2690980-2790307	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	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
9	nsv1032667	chr9:2691667-2788242	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1019973	chr9:2691812-2790419	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv539935	chr9:2691812-2790419	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	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
13	nsv1021572	chr9:2703159-2790123	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	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
15	nsv1033982	chr9:2724666-2780665	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv539936	chr9:2724666-2780665	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	nsv1023850	chr9:2736931-2790123	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
18	nsv466087	chr9:2746548-2790307	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	nsv613142	chr9:2746548-2790307	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	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
21	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

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2718000-2772800	Weak transcription	Aorta	Aorta
2	chr9:2728600-2772400	Weak transcription	Brain Hippocampus Middle	brain
3	chr9:2737200-2777000	Weak transcription	Esophagus	oesophagus
4	chr9:2745800-2771600	Weak transcription	Brain Anterior Caudate	brain
5	chr9:2746400-2772800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:2746800-2773200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:2752200-2777000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:2755400-2772200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:2759400-2773000	Weak transcription	Fetal Brain Male	brain
10	chr9:2759600-2776800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:2760200-2777000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr9:2760600-2773000	Weak transcription	Psoas Muscle	Psoas
13	chr9:2763000-2772800	Weak transcription	Fetal Kidney	kidney
14	chr9:2764200-2775400	Weak transcription	Thymus	Thymus
15	chr9:2764800-2774200	Weak transcription	Brain Substantia Nigra	brain
16	chr9:2765800-2771000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:2765800-2771600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr9:2765800-2772800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:2765800-2791200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr9:2766000-2771000	Weak transcription	Fetal Heart	heart
21	chr9:2766000-2771000	Weak transcription	Fetal Lung	lung
22	chr9:2766000-2771200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:2766000-2771800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr9:2766000-2771800	Weak transcription	Placenta	Placenta
25	chr9:2766000-2773000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr9:2766000-2774600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr9:2766000-2775800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:2766000-2777000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:2766000-2777000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr9:2766200-2771800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:2766200-2772200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr9:2766200-2772800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:2766800-2773200	Weak transcription	Brain Angular Gyrus	brain
34	chr9:2767000-2771800	Weak transcription	Liver	Liver
35	chr9:2767800-2773000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:2767800-2773200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr9:2767800-2775600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr9:2768000-2772800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr9:2768000-2779200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:2768200-2771600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr9:2768200-2782600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:2768400-2771200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr9:2768400-2771200	Strong transcription	HMEC	breast
44	chr9:2768400-2771400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:2768400-2771800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:2768400-2771800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:2768400-2772000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr9:2768400-2773200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr9:2768400-2773600	Strong transcription	Primary T cells from cord blood	blood
50	chr9:2768400-2774400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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