Variant report

Variant	rs1405847
Chromosome Location	chr6:72125053-72125054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B3GAT2-3	chr6:72124149-72126262	ENSG00000233237
2	lnc-B3GAT2-3	chr6:72123954-72126262	XLOC_005764
3	lnc-B3GAT2-3	chr6:72124149-72126262	XLOC_005764
4	lnc-B3GAT2-3	chr6:72123874-72126262	NONHSAT113497
5	lnc-B3GAT2-3	chr6:72124148-72126262	ENSG00000233237.2

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10485017	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs1192035	1.00[ASN][1000 genomes]
rs1192036	1.00[ASN][1000 genomes]
rs1192039	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1192041	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1192042	1.00[ASN][1000 genomes]
rs1192043	1.00[ASN][1000 genomes]
rs1192044	1.00[ASN][1000 genomes]
rs1358379	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1405849	0.89[AFR][1000 genomes]
rs1527709	0.90[AFR][1000 genomes]
rs1527710	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1527711	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs16881296	0.93[AFR][1000 genomes]
rs35217364	0.89[AFR][1000 genomes]
rs701695	1.00[ASN][1000 genomes]
rs73520608	1.00[ASN][1000 genomes]
rs765466	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765945	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs828639	1.00[ASN][1000 genomes]
rs828640	1.00[ASN][1000 genomes]
rs828641	1.00[ASN][1000 genomes]
rs828643	1.00[ASN][1000 genomes]
rs828645	1.00[ASN][1000 genomes]
rs828646	1.00[ASN][1000 genomes]
rs9446370	1.00[JPT][hapmap]
rs9446392	1.00[JPT][hapmap];0.90[TSI][hapmap]
rs9446393	1.00[JPT][hapmap]
rs980027	0.88[MKK][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830684	chr6:72094842-72282684	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	488 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:72106400-72126800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:72106400-72128600	Weak transcription	Fetal Brain Male	brain
3	chr6:72106800-72128600	Weak transcription	Fetal Brain Female	brain
4	chr6:72106800-72128800	Weak transcription	Brain Germinal Matrix	brain
5	chr6:72115400-72125200	Weak transcription	Fetal Intestine Large	intestine
6	chr6:72116200-72128600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:72117600-72128000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:72118200-72127800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:72119800-72125200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:72120000-72129000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:72120200-72126600	Weak transcription	Fetal Intestine Small	intestine
12	chr6:72120200-72126600	Weak transcription	Lung	lung
13	chr6:72122000-72125200	Genic enhancers	HSMM	muscle
14	chr6:72122400-72127400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:72122400-72128800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:72122600-72125200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:72122600-72126000	Weak transcription	Fetal Stomach	stomach
18	chr6:72122600-72126800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:72122600-72126800	Weak transcription	Spleen	Spleen
20	chr6:72122600-72127400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:72122600-72128200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:72122600-72128800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:72122600-72129000	Weak transcription	Gastric	stomach
24	chr6:72122800-72125200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:72122800-72125200	Active TSS	A549	lung
26	chr6:72123400-72128600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:72123600-72125400	Genic enhancers	HUVEC	blood vessel
28	chr6:72123600-72127200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:72123800-72125200	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr6:72124000-72125200	Enhancers	Fetal Heart	heart
31	chr6:72124000-72125600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
32	chr6:72124200-72125200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
33	chr6:72124200-72125400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:72124200-72125800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:72124200-72126200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:72124200-72127000	Strong transcription	NHDF-Ad	bronchial
37	chr6:72124200-72127200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:72124200-72127200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:72124400-72125200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
40	chr6:72124400-72125200	Genic enhancers	NH-A	brain
41	chr6:72124400-72125200	Genic enhancers	NHLF	lung
42	chr6:72124400-72125400	Genic enhancers	HSMMtube	muscle
43	chr6:72124400-72127200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:72124400-72127200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:72124400-72127200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:72124400-72127200	Strong transcription	Placenta	Placenta
47	chr6:72124600-72125800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:72124600-72126000	Weak transcription	Right Atrium	heart
49	chr6:72124600-72126600	Genic enhancers	Fetal Kidney	kidney
50	chr6:72124600-72127200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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