Variant report

Variant	rs7648887
Chromosome Location	chr3:196181269-196181270
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBXO45-4	chr3:196181233-196181272	NONHSAT094341

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11185540	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11185541	0.98[ASN][1000 genomes]
rs1872353	1.00[ASW][hapmap]
rs3973	0.87[CEU][hapmap]
rs4916427	0.87[CEU][hapmap]
rs4916497	0.82[CEU][hapmap]
rs62409230	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6802616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7372951	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864836	0.82[CEU][hapmap]
rs9877304	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv1003764	chr3:196028141-196190687	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv536895	chr3:196028141-196190687	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	esv1844755	chr3:196057616-196190350	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
13	nsv878184	chr3:196158773-196191434	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv878185	chr3:196158773-196199204	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv878186	chr3:196158773-196219794	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv527402	chr3:196168101-196187608	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	esv3349428	chr3:196168691-196197042	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7648887	UBXD7	Cis_1M	lymphoblastoid	RTeQTL
rs7648887	PCYT1A	cis	parietal	SCAN
rs7648887	RNF168	cis	cerebellum	SCAN
rs7648887	TCTEX1D2	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196168200-196184400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:196168400-196194200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:196170800-196196000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:196171000-196198400	Weak transcription	Fetal Brain Female	brain
5	chr3:196171400-196198600	Weak transcription	Ovary	ovary
6	chr3:196171600-196191000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:196171800-196181600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:196171800-196197600	Weak transcription	Brain Anterior Caudate	brain
9	chr3:196171800-196198200	Weak transcription	NHDF-Ad	bronchial
10	chr3:196172200-196184600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:196172200-196184600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:196172200-196198200	Weak transcription	Aorta	Aorta
13	chr3:196173000-196198600	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:196173200-196198200	Weak transcription	Brain Angular Gyrus	brain
15	chr3:196174800-196195200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:196174800-196198200	Weak transcription	Right Ventricle	heart
17	chr3:196175200-196187000	Weak transcription	Lung	lung
18	chr3:196175200-196198200	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:196175200-196198400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:196175600-196181600	Weak transcription	Primary T cells from cord blood	blood
21	chr3:196176200-196181600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:196177000-196181600	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:196177000-196198400	Weak transcription	Pancreas	Pancrea
24	chr3:196177200-196198200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:196177400-196195400	Weak transcription	Liver	Liver
26	chr3:196177800-196181400	Weak transcription	Left Ventricle	heart
27	chr3:196177800-196198200	Weak transcription	Gastric	stomach
28	chr3:196177800-196198600	Weak transcription	Small Intestine	intestine
29	chr3:196178000-196191400	Weak transcription	Fetal Stomach	stomach
30	chr3:196178200-196191400	Weak transcription	Thymus	Thymus
31	chr3:196178200-196195800	Weak transcription	Dnd41	blood
32	chr3:196178200-196197400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:196178200-196197600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:196178200-196198000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:196178200-196198400	Weak transcription	Brain Germinal Matrix	brain
36	chr3:196178200-196198600	Weak transcription	Psoas Muscle	Psoas
37	chr3:196180000-196181600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:196180000-196194000	Weak transcription	Fetal Thymus	thymus
39	chr3:196180400-196194200	Weak transcription	Primary B cells from cord blood	blood
40	chr3:196180400-196197400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:196180600-196197400	Weak transcription	Adipose Nuclei	Adipose
42	chr3:196180600-196198400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:196181000-196182400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr3:196181000-196183000	Strong transcription	Brain Cingulate Gyrus	brain
45	chr3:196181200-196182800	Weak transcription	GM12878-XiMat	blood

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