Variant report

Variant	rs2240574
Chromosome Location	chr7:12610937-12610938
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VWDE-1	chr7:12610831-12611017	ENSG00000225606.1

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10248988	0.96[CEU][hapmap]
rs10255606	0.96[CEU][hapmap]
rs10276226	0.87[CEU][hapmap]
rs1034856	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11973033	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17283514	0.96[CEU][hapmap]
rs17283717	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs17355921	0.81[ASN][1000 genomes]
rs1859989	0.88[CEU][hapmap]
rs1859990	0.88[CEU][hapmap]
rs1990223	0.80[EUR][1000 genomes]
rs2215063	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs2240571	0.92[CEU][hapmap];0.81[YRI][hapmap]
rs2240572	0.93[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs2240575	0.81[EUR][1000 genomes]
rs3173628	0.96[CEU][hapmap]
rs3735222	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3735223	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs41356146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs41379149	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4458754	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs55682719	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55829483	0.83[ASN][1000 genomes]
rs55999874	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56085455	0.83[ASN][1000 genomes]
rs56274604	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56760264	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6460964	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6460965	0.96[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6460967	0.96[CEU][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes]
rs6954111	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6954578	0.88[CEU][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes]
rs6965970	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6967031	0.94[JPT][hapmap]
rs6972418	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73060662	0.85[ASN][1000 genomes]
rs73060664	0.85[ASN][1000 genomes]
rs73060678	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73060679	0.83[ASN][1000 genomes]
rs73060680	0.80[ASN][1000 genomes]
rs73060684	0.98[ASN][1000 genomes]
rs73060686	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73062610	0.83[ASN][1000 genomes]
rs73062611	0.83[ASN][1000 genomes]
rs73062639	0.84[ASN][1000 genomes]
rs7782451	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7799976	0.80[ASN][1000 genomes]
rs7801351	0.96[CEU][hapmap]
rs7803810	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7804260	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7811582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968792	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1030764	chr7:12532287-12710429	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv528031	chr7:12536336-12618764	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1025397	chr7:12543161-12612059	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1025006	chr7:12543161-12618924	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027831	chr7:12543161-12619740	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv470066	chr7:12543794-12618764	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1033478	chr7:12547121-12618924	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv464379	chr7:12572742-12618764	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv606231	chr7:12572742-12618764	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1018053	chr7:12580554-12632996	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1020242	chr7:12605593-12641202	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2240574	SCIN	Cis_1M	lymphoblastoid	RTeQTL
rs2240574	SCIN	cis	Thyroid	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12609400-12611000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr7:12609400-12611000	Enhancers	Spleen	Spleen
3	chr7:12609400-12611000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
4	chr7:12609400-12611600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr7:12609600-12611000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
6	chr7:12609600-12611200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr7:12609600-12611200	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr7:12609600-12611200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
9	chr7:12609600-12612000	Active TSS	Brain Anterior Caudate	brain
10	chr7:12609800-12611000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:12609800-12611000	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
15	chr7:12609800-12611000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr7:12609800-12611000	Bivalent Enhancer	Liver	Liver
18	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
19	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
20	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
21	chr7:12609800-12611000	Active TSS	K562	blood
22	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
23	chr7:12609800-12611000	Flanking Bivalent TSS/Enh	NH-A	brain
24	chr7:12609800-12611200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr7:12609800-12611200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
26	chr7:12609800-12611200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr7:12609800-12611200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr7:12609800-12611200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
29	chr7:12609800-12611200	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
30	chr7:12609800-12611600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr7:12610000-12611000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:12610000-12611000	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:12610000-12611000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr7:12610000-12611000	Flanking Active TSS	Esophagus	oesophagus
35	chr7:12610000-12611000	Flanking Active TSS	Pancreas	Pancrea
36	chr7:12610000-12611000	Bivalent/Poised TSS	A549	lung
37	chr7:12610000-12611000	Bivalent/Poised TSS	NHDF-Ad	bronchial
38	chr7:12610000-12611200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:12610000-12611200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
40	chr7:12610200-12611000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr7:12610200-12611000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr7:12610200-12611000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
43	chr7:12610200-12611000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
44	chr7:12610200-12611000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr7:12610200-12611000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
46	chr7:12610200-12611200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
47	chr7:12610200-12611200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:12610200-12611200	Bivalent/Poised TSS	Small Intestine	intestine
49	chr7:12610200-12611600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr7:12610200-12612000	Active TSS	Rectal Mucosa Donor 31	rectum

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