Variant report

Variant	rs1404416
Chromosome Location	chr7:17814272-17814273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HDAC9-11	chr7:17812631-17814939	NONHSAT119344

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10249221	0.91[ASN][1000 genomes]
rs10264355	1.00[ASN][1000 genomes]
rs10264445	0.91[ASN][1000 genomes]
rs10264447	0.91[ASN][1000 genomes]
rs1404417	1.00[ASN][1000 genomes]
rs1404418	1.00[ASN][1000 genomes]
rs1404419	1.00[ASN][1000 genomes]
rs1404421	0.99[ASN][1000 genomes]
rs1404425	0.94[ASN][1000 genomes]
rs1830006	0.94[ASN][1000 genomes]
rs1880457	0.82[YRI][hapmap]
rs1965534	0.96[ASN][1000 genomes]
rs1997019	0.94[ASN][1000 genomes]
rs2068172	1.00[ASN][1000 genomes]
rs2110015	0.97[ASN][1000 genomes]
rs2254361	1.00[ASN][1000 genomes]
rs2254594	1.00[ASN][1000 genomes]
rs2254737	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs2537592	1.00[ASN][1000 genomes]
rs2537593	1.00[ASN][1000 genomes]
rs2537594	1.00[ASN][1000 genomes]
rs2691556	1.00[ASN][1000 genomes]
rs2691559	0.87[YRI][hapmap]
rs2691581	0.96[ASN][1000 genomes]
rs2691582	0.96[ASN][1000 genomes]
rs2691584	1.00[ASN][1000 genomes]
rs2691592	1.00[ASN][1000 genomes]
rs2691593	1.00[ASN][1000 genomes]
rs2691595	1.00[ASN][1000 genomes]
rs2691596	1.00[ASN][1000 genomes]
rs2691597	0.86[YRI][hapmap]
rs2691600	0.88[YRI][hapmap]
rs2691604	1.00[ASN][1000 genomes]
rs2691609	0.88[YRI][hapmap]
rs2691610	1.00[ASN][1000 genomes]
rs2691615	0.88[YRI][hapmap]
rs2691616	1.00[ASN][1000 genomes]
rs2691617	1.00[ASN][1000 genomes]
rs2723503	1.00[ASN][1000 genomes]
rs2723504	0.85[YRI][hapmap]
rs2723505	0.85[YRI][hapmap]
rs2723506	1.00[ASN][1000 genomes]
rs2723507	1.00[ASN][1000 genomes]
rs2723508	1.00[ASN][1000 genomes]
rs2723509	1.00[ASN][1000 genomes]
rs2723510	1.00[ASN][1000 genomes]
rs2723511	1.00[ASN][1000 genomes]
rs2723513	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2723514	1.00[ASN][1000 genomes]
rs2723516	1.00[ASN][1000 genomes]
rs2723517	1.00[ASN][1000 genomes]
rs2723518	1.00[ASN][1000 genomes]
rs2723519	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2723520	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2723521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723572	0.88[YRI][hapmap]
rs4316058	0.92[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][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	nsv869352	chr7:17237983-17932878	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1021524	chr7:17251148-17963307	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1021289	chr7:17254117-17873816	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv538754	chr7:17254117-17873816	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv534309	chr7:17254118-17932878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv533938	chr7:17254118-18040301	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv887804	chr7:17571140-17885468	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1024398	chr7:17630148-18545073	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
9	nsv538764	chr7:17630148-18545073	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
10	esv2764016	chr7:17800816-17815402	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv12823	chr7:17813669-17814724	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17810200-17815000	Enhancers	HMEC	breast
2	chr7:17812000-17814400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:17812000-17814400	Enhancers	NHLF	lung
4	chr7:17812000-17814600	Enhancers	NHDF-Ad	bronchial
5	chr7:17812000-17815000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr7:17812000-17815200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:17812200-17814600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:17812200-17815200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:17812200-17815400	Enhancers	NH-A	brain
10	chr7:17812400-17814400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:17812400-17814600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:17812400-17815000	Enhancers	Osteobl	bone
13	chr7:17812400-17846200	Weak transcription	Fetal Stomach	stomach
14	chr7:17812400-17852200	Weak transcription	Esophagus	oesophagus
15	chr7:17812600-17814600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:17812600-17887600	Weak transcription	Gastric	stomach
17	chr7:17813000-17815000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:17813400-17814800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr7:17813400-17814800	Weak transcription	Placenta	Placenta
20	chr7:17813400-17815000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr7:17813400-17821200	Weak transcription	Thymus	Thymus
22	chr7:17813600-17879200	Weak transcription	HSMMtube	muscle
23	chr7:17813800-17815400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:17813800-17833200	Weak transcription	Fetal Thymus	thymus
25	chr7:17813800-17836200	Weak transcription	HSMM	muscle
26	chr7:17814200-17814400	Flanking Active TSS	Fetal Heart	heart
27	chr7:17814200-17814800	Weak transcription	Left Ventricle	heart
28	chr7:17814200-17833200	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links