Variant report

Variant	rs7033946
Chromosome Location	chr9:2796867-2796868
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	chr9:2796574-2797685	NONHSAT130010

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10046804	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10113893	0.86[EUR][1000 genomes]
rs10118386	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10122155	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10122896	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10125062	0.80[ASN][1000 genomes]
rs10125412	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10757686	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10757691	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10812641	0.96[CEU][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs6476022	0.80[ASN][1000 genomes]
rs6476023	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7031607	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7032942	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7037204	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7041669	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7042249	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7049072	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7857106	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7865866	0.87[AMR][1000 genomes];0.83[EUR][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	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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2775000-2801600	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:2777800-2800000	Weak transcription	Colonic Mucosa	Colon
3	chr9:2778000-2801600	Weak transcription	Small Intestine	intestine
4	chr9:2778000-2801800	Weak transcription	Gastric	stomach
5	chr9:2778000-2803200	Weak transcription	Aorta	Aorta
6	chr9:2778400-2800200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:2778600-2801400	Weak transcription	Fetal Brain Male	brain
8	chr9:2778600-2801600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:2778800-2798200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:2778800-2799600	Weak transcription	Brain Angular Gyrus	brain
11	chr9:2778800-2800000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:2778800-2802800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr9:2779200-2801600	Weak transcription	Brain Substantia Nigra	brain
14	chr9:2782400-2800800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:2783200-2798800	Weak transcription	Fetal Kidney	kidney
16	chr9:2786400-2797000	Weak transcription	Fetal Heart	heart
17	chr9:2786400-2800400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:2787200-2802200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:2787600-2808000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:2787800-2798400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:2787800-2801800	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr9:2787800-2812200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr9:2788200-2800200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:2788400-2809400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr9:2789000-2798000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:2789000-2809000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:2789400-2798600	Strong transcription	Osteobl	bone
28	chr9:2790400-2798000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr9:2790600-2800200	Strong transcription	NHEK	skin
30	chr9:2791400-2798200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr9:2791600-2798000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr9:2791600-2798400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr9:2791600-2800000	Weak transcription	Placenta	Placenta
34	chr9:2791600-2815800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr9:2791800-2797600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:2791800-2797800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:2791800-2798000	Weak transcription	HepG2	liver
38	chr9:2791800-2798800	Weak transcription	Esophagus	oesophagus
39	chr9:2791800-2800200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr9:2791800-2800200	Weak transcription	Brain Germinal Matrix	brain
41	chr9:2791800-2801400	Weak transcription	Right Ventricle	heart
42	chr9:2791800-2801600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr9:2791800-2801800	Weak transcription	Pancreas	Pancrea
44	chr9:2791800-2821800	Strong transcription	Primary T cells from cord blood	blood
45	chr9:2792000-2797800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr9:2792000-2797800	Weak transcription	Left Ventricle	heart
47	chr9:2792000-2800200	Weak transcription	Fetal Brain Female	brain
48	chr9:2792000-2800200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr9:2792000-2800400	Weak transcription	Spleen	Spleen
50	chr9:2792000-2801800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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