Variant report

Variant	rs2505658
Chromosome Location	chr6:2329626-2329627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WRNIP1-2	chr6:2329517-2329638	ENSG00000250903
2	lnc-WRNIP1-2	chr6:2329517-2329986	XLOC_005126

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11242758	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11961324	0.84[ASN][1000 genomes]
rs11962550	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11963138	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11963529	0.86[ASN][1000 genomes]
rs12191002	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12661136	0.92[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs13196306	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13217030	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2295008	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2450299	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2450304	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2450307	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2450310	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2479001	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2479002	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2479004	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2479008	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2479011	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2479014	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505657	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505659	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505660	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505661	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505662	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505663	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505666	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505667	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505670	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505671	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505673	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505677	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505678	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778568	0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs3800184	1.00[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs3800185	0.92[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3800187	0.86[ASN][1000 genomes]
rs3800190	0.92[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs3823287	0.92[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs55992523	0.85[ASN][1000 genomes]
rs56196406	0.86[ASN][1000 genomes]
rs6596879	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72830182	0.84[ASN][1000 genomes]
rs72830184	0.86[ASN][1000 genomes]
rs7754950	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9328087	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9378686	0.92[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs9378687	0.92[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs9378688	1.00[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9378692	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9378693	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9391946	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9392373	0.82[ASN][1000 genomes]
rs9392374	0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs9392375	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs9392377	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9405550	1.00[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
5	nsv1017174	chr6:2213893-2340529	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
7	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
8	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2505658	WRNIP1	cis	parietal	SCAN
rs2505658	LOC728772///TMEM106A	trans	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2317200-2338800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:2319600-2329800	Weak transcription	HSMMtube	muscle
3	chr6:2321000-2331200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:2325800-2334200	Weak transcription	Gastric	stomach
5	chr6:2328200-2338200	Weak transcription	Liver	Liver
6	chr6:2329200-2330400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
7	chr6:2329200-2330400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
8	chr6:2329200-2330600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:2329200-2330600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
10	chr6:2329400-2330200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr6:2329400-2330200	ZNF genes & repeats	Fetal Intestine Large	intestine
12	chr6:2329400-2330400	ZNF genes & repeats	Fetal Muscle Leg	muscle
13	chr6:2329400-2330400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
14	chr6:2329600-2330200	ZNF genes & repeats	Primary B cells from cord blood	blood
15	chr6:2329600-2334400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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