Variant report

Variant	rs9962121
Chromosome Location	chr18:29076717-29076718
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:28680816..28682711-chr18:29076315..29078384,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B4GALT6-2	chr18:29076608-29076815	ENSG00000266521.1

Variant related genes	Relation type
ENSG00000134755	Chromatin interaction
ENSG00000265888	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1031729	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1350731	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1460602	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17660585	0.98[ASN][1000 genomes]
rs1824477	0.92[ASN][1000 genomes]
rs1841396	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2212617	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2212618	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2219584	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2704050	0.90[CHB][hapmap];0.95[CHD][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs2704051	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs2704052	0.90[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs2704053	0.95[ASN][1000 genomes]
rs2704055	0.86[ASN][1000 genomes]
rs2848677	0.95[ASN][1000 genomes]
rs2848680	0.95[ASN][1000 genomes]
rs2848681	0.95[ASN][1000 genomes]
rs4799310	0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs4799573	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6506927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6506928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7227343	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7227984	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs7231288	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7231553	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7232282	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7235272	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7236324	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7236469	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs7238729	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7239805	0.86[ASN][1000 genomes]
rs7240824	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7240920	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7241107	0.92[ASN][1000 genomes]
rs73414280	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73953901	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9304098	0.84[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs9304099	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs9941421	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9945031	0.89[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs9945420	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9951843	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9961910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9961920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9961925	1.00[ASN][1000 genomes]
rs9962318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9962333	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9962423	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats 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 miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9962121	RP11-650P15.1	cis	Thyroid	GTEx
rs9962121	DSC1	cis	parietal	SCAN
rs9962121	RP11-650P15.1	cis	Heart Left Ventricle	GTEx
rs9962121	DSG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29067600-29076800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr18:29071200-29077200	Weak transcription	Fetal Intestine Small	intestine
3	chr18:29071800-29077400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr18:29071800-29077400	Weak transcription	HMEC	breast
5	chr18:29072000-29077200	Weak transcription	NHEK	skin
6	chr18:29072000-29077400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr18:29072200-29077600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr18:29074200-29077200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr18:29074400-29077400	Weak transcription	GM12878-XiMat	blood
10	chr18:29074800-29077400	Weak transcription	Colonic Mucosa	Colon
11	chr18:29075200-29077200	Weak transcription	K562	blood

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