Variant report

Variant	rs331419
Chromosome Location	chr18:7815417-7815418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC30-4	chr18:7814116-7815728	ENSG00000264596.1

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10502362	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs1117814	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12965898	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1348104	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1440995	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs1440999	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1441000	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs1441001	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1443614	0.84[CEU][hapmap]
rs1443616	0.88[CEU][hapmap]
rs1822456	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2009770	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs2197010	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2377575	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2377577	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs331414	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331415	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331425	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs331426	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34294315	0.84[EUR][1000 genomes]
rs36188935	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs364418	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385769	0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4798598	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4798599	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs631574	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638251	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6506535	0.88[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs671369	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs694096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7228457	0.86[EUR][1000 genomes]
rs7232793	0.84[EUR][1000 genomes]
rs7233704	0.84[EUR][1000 genomes]
rs7235300	0.81[CEU][hapmap]
rs7239136	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7243673	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs727949	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs727951	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8083298	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8089088	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8098502	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9944547	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv458016	chr18:7488133-7934001	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv576399	chr18:7488133-7934001	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2762810	chr18:7492090-7924728	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv576425	chr18:7747873-7859757	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1062454	chr18:7784432-7838015	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7810200-7817600	Weak transcription	Ovary	ovary
2	chr18:7810200-7822400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr18:7810200-7824200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr18:7812600-7816400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr18:7813200-7822600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr18:7813400-7815600	ZNF genes & repeats	Thymus	Thymus
7	chr18:7813400-7816000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr18:7814000-7815600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr18:7814000-7815600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr18:7814000-7815800	ZNF genes & repeats	Fetal Stomach	stomach
11	chr18:7814000-7816000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr18:7814200-7815600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr18:7814200-7815600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr18:7814200-7815600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr18:7814600-7815800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr18:7814600-7821400	Weak transcription	Fetal Heart	heart
17	chr18:7815400-7815600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
18	chr18:7815400-7815800	Weak transcription	Liver	Liver
19	chr18:7815400-7817000	Weak transcription	Left Ventricle	heart
20	chr18:7815400-7817800	Weak transcription	Right Ventricle	heart
21	chr18:7815400-7819400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr18:7815400-7820000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr18:7815400-7820600	Weak transcription	Psoas Muscle	Psoas
24	chr18:7815400-7821800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr18:7815400-7822600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr18:7815400-7843800	Weak transcription	A549	lung

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