Variant report

Variant	rs9386136
Chromosome Location	chr6:146158300-146158301
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:146134408..146136747-chr6:146158257..146160540,2	MCF-7	breast:
2	chr6:146131042..146132915-chr6:146157627..146159920,2	K562	blood:
3	chr6:146054185..146056773-chr6:146157994..146159853,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBXO30-1	chr6:146156331-146158701	l_3286_chr6:146156330-146160471_brain

Variant related genes	Relation type
ENSG00000235652	Chromatin interaction
ENSG00000112425	Chromatin interaction
ENSG00000118496	Chromatin interaction
ENSG00000270638	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1011597	0.95[JPT][hapmap]
rs10223507	0.85[JPT][hapmap]
rs1062068	0.85[JPT][hapmap]
rs1070518	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10872580	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs12199362	0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs1292333	0.95[JPT][hapmap]
rs1292334	0.95[JPT][hapmap]
rs1337841	0.95[JPT][hapmap]
rs1415744	0.95[JPT][hapmap]
rs1415746	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1415747	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1890170	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1890171	0.95[JPT][hapmap]
rs1970306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2050027	0.95[JPT][hapmap]
rs2064185	0.94[JPT][hapmap]
rs2142978	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2142980	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2206142	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2223411	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2224120	0.85[JPT][hapmap]
rs2235481	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2246132	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247666	0.85[JPT][hapmap]
rs2249386	0.85[JPT][hapmap]
rs2253654	0.85[JPT][hapmap]
rs2253757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2265475	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2328709	0.80[ASN][1000 genomes]
rs2485631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2814874	0.85[JPT][hapmap]
rs2814875	0.85[JPT][hapmap]
rs2814877	0.86[JPT][hapmap]
rs34541797	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3811102	0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs3924499	0.85[JPT][hapmap]
rs3924502	0.86[JPT][hapmap]
rs4075694	0.86[JPT][hapmap]
rs4280983	0.86[JPT][hapmap];0.94[YRI][hapmap]
rs4398765	0.83[ASN][1000 genomes]
rs4895683	0.95[JPT][hapmap]
rs4896832	0.95[JPT][hapmap]
rs4896837	0.95[JPT][hapmap]
rs4896838	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4896844	0.81[ASN][1000 genomes]
rs62435775	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570708	0.95[JPT][hapmap]
rs6570713	0.81[ASN][1000 genomes]
rs6570732	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6900175	0.92[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6901888	0.95[JPT][hapmap]
rs6906258	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6906402	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6912351	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6915718	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6922507	0.86[JPT][hapmap]
rs6923545	0.85[JPT][hapmap]
rs6930154	0.95[JPT][hapmap]
rs6931553	0.80[ASN][1000 genomes]
rs697053	0.95[JPT][hapmap]
rs697054	0.95[JPT][hapmap]
rs697055	0.95[JPT][hapmap]
rs702304	0.95[JPT][hapmap]
rs702306	0.95[JPT][hapmap]
rs702307	0.95[JPT][hapmap]
rs702316	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs702318	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs702319	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs702322	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs702324	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7746618	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7752286	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7753092	0.86[JPT][hapmap];0.94[YRI][hapmap]
rs7753273	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7753696	0.86[JPT][hapmap]
rs7753770	0.95[JPT][hapmap]
rs857875	0.95[JPT][hapmap]
rs857877	0.95[JPT][hapmap]
rs857880	0.95[JPT][hapmap]
rs857881	0.95[JPT][hapmap]
rs857882	0.95[JPT][hapmap]
rs857883	0.95[JPT][hapmap]
rs863820	0.85[JPT][hapmap]
rs9285508	0.89[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs9373467	0.83[EUR][1000 genomes]
rs9373475	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs9376961	0.95[JPT][hapmap]
rs9376965	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376970	0.85[JPT][hapmap];0.94[YRI][hapmap]
rs9386132	0.80[ASN][1000 genomes]
rs9386134	0.80[ASN][1000 genomes]
rs9390356	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs9390365	0.86[JPT][hapmap]
rs9403737	0.95[JPT][hapmap]
rs9403739	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9403742	0.85[JPT][hapmap]
rs9403749	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs9403756	0.85[JPT][hapmap]
rs9485017	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9497395	0.81[JPT][hapmap]
rs9497403	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9497426	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs9497431	0.86[JPT][hapmap];0.94[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830835	chr6:146145148-146287473	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146136800-146165200	Weak transcription	Lung	lung
2	chr6:146137400-146167200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:146137800-146159600	Weak transcription	Psoas Muscle	Psoas
4	chr6:146137800-146163000	Weak transcription	Fetal Stomach	stomach
5	chr6:146150600-146163000	Weak transcription	Left Ventricle	heart
6	chr6:146150600-146171200	Weak transcription	Aorta	Aorta
7	chr6:146150600-146174000	Weak transcription	Right Ventricle	heart
8	chr6:146156200-146158400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr6:146156600-146158400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr6:146156800-146158800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:146157000-146158400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:146157200-146158400	Enhancers	Hela-S3	cervix
13	chr6:146157200-146158400	Enhancers	NHEK	skin
14	chr6:146157200-146158600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:146157600-146158400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:146157600-146158800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:146157600-146158800	Weak transcription	Placenta	Placenta
18	chr6:146157600-146163200	Weak transcription	Brain Germinal Matrix	brain
19	chr6:146157800-146158400	Enhancers	NHDF-Ad	bronchial
20	chr6:146157800-146158800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:146157800-146159000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:146157800-146159200	Weak transcription	HMEC	breast
23	chr6:146157800-146159400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:146157800-146159400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:146157800-146162800	Weak transcription	Gastric	stomach
26	chr6:146158000-146159000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:146158000-146159000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:146158000-146159200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:146158000-146163400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:146158200-146159400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:146158200-146159400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:146158200-146159600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:146158200-146163600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:146158200-146163600	Weak transcription	HSMMtube	muscle
35	chr6:146158200-146163600	Weak transcription	Osteobl	bone
36	chr6:146158200-146164200	Weak transcription	Brain Anterior Caudate	brain
37	chr6:146158200-146166000	Weak transcription	Muscle Satellite Cultured Cells	--

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