Variant report

Variant	rs1060812
Chromosome Location	chr9:2783788-2783789
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RFX3-3	chr9:2783674-2784301	NONHSAT130010

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10121371	0.89[EUR][1000 genomes]
rs10738777	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10738778	0.82[ASN][1000 genomes]
rs10738782	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10757675	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10812639	0.89[EUR][1000 genomes]
rs10812668	0.83[EUR][1000 genomes]
rs1454635	0.92[EUR][1000 genomes]
rs1551410	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2168134	0.89[ASN][1000 genomes]
rs2168135	0.92[EUR][1000 genomes]
rs4520217	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4623490	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4740699	0.92[EUR][1000 genomes]
rs4741767	0.91[EUR][1000 genomes]
rs6476018	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7027337	0.92[EUR][1000 genomes]
rs7035082	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7037223	0.80[EUR][1000 genomes]
rs7038516	0.86[AMR][1000 genomes]
rs7041159	0.81[EUR][1000 genomes]
rs7849358	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7850616	0.85[EUR][1000 genomes]
rs7869344	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
16	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
17	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
18	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
19	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
20	nsv1032474	chr9:2773573-2804799	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	n/a	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	chr9:2765800-2791200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:2770600-2789800	Weak transcription	Hela-S3	cervix
3	chr9:2773200-2784800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:2773600-2787200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:2775000-2801600	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:2776000-2785400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:2777200-2790800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr9:2777800-2785000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr9:2777800-2787200	Weak transcription	Placenta	Placenta
10	chr9:2777800-2791600	Weak transcription	Right Ventricle	heart
11	chr9:2777800-2800000	Weak transcription	Colonic Mucosa	Colon
12	chr9:2778000-2787200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:2778000-2787400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:2778000-2788400	Weak transcription	Lung	lung
15	chr9:2778000-2789400	Weak transcription	Fetal Intestine Large	intestine
16	chr9:2778000-2790000	Strong transcription	A549	lung
17	chr9:2778000-2790800	Weak transcription	Esophagus	oesophagus
18	chr9:2778000-2790800	Weak transcription	Pancreas	Pancrea
19	chr9:2778000-2790800	Weak transcription	Thymus	Thymus
20	chr9:2778000-2791000	Weak transcription	Spleen	Spleen
21	chr9:2778000-2794400	Weak transcription	Psoas Muscle	Psoas
22	chr9:2778000-2801600	Weak transcription	Small Intestine	intestine
23	chr9:2778000-2801800	Weak transcription	Gastric	stomach
24	chr9:2778000-2803200	Weak transcription	Aorta	Aorta
25	chr9:2778200-2789200	Weak transcription	Fetal Thymus	thymus
26	chr9:2778400-2784200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:2778400-2785600	Weak transcription	Ovary	ovary
28	chr9:2778400-2786200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:2778400-2787400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:2778400-2791000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr9:2778400-2800200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:2778600-2787400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr9:2778600-2787400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr9:2778600-2787600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:2778600-2788000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr9:2778600-2789400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr9:2778600-2789400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr9:2778600-2790000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr9:2778600-2801400	Weak transcription	Fetal Brain Male	brain
40	chr9:2778600-2801600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr9:2778800-2785000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:2778800-2785000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr9:2778800-2785200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr9:2778800-2787200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:2778800-2787200	Weak transcription	Brain Germinal Matrix	brain
46	chr9:2778800-2787400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:2778800-2789400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr9:2778800-2790800	Weak transcription	HepG2	liver
49	chr9:2778800-2791000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:2778800-2791000	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links