Variant report

Variant	rs2840294
Chromosome Location	chr1:113668998-113668999
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113614064..113616964-chr1:113668302..113669880,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC16A1-5	chr1:113667943-113669505	NONHSAT005317

Variant related genes	Relation type
ENSG00000238198	Chromatin interaction
ENSG00000198799	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11102581	0.88[EUR][1000 genomes]
rs11102582	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs1216760	0.85[EUR][1000 genomes]
rs1216762	0.83[EUR][1000 genomes]
rs1216763	0.83[EUR][1000 genomes]
rs1216768	0.87[EUR][1000 genomes]
rs1216780	0.82[EUR][1000 genomes]
rs1216781	0.96[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs1216801	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1216804	0.88[EUR][1000 genomes]
rs12568813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12744009	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs12758163	0.82[EUR][1000 genomes]
rs1619133	0.90[EUR][1000 genomes]
rs1626085	0.86[EUR][1000 genomes]
rs17030974	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1728230	0.86[EUR][1000 genomes]
rs1728238	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1766862	0.88[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs1766863	0.89[EUR][1000 genomes]
rs1778015	0.83[EUR][1000 genomes]
rs1778018	0.89[EUR][1000 genomes]
rs1778024	0.96[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs1778025	0.96[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs1778027	0.89[EUR][1000 genomes]
rs1778028	0.81[EUR][1000 genomes]
rs2485964	0.89[EUR][1000 genomes]
rs2798686	0.86[EUR][1000 genomes]
rs4025965	0.86[EUR][1000 genomes]
rs72683488	0.82[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	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
7	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
8	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
9	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
10	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2840294	LRIG2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113633600-113672600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:113633800-113670000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:113633800-113672600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:113634200-113669800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:113634200-113669800	Strong transcription	Primary B cells from peripheral blood	blood
6	chr1:113634200-113670000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:113634200-113671400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:113634200-113673000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:113634400-113672600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:113634600-113669800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:113634600-113669800	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:113634600-113669800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:113634600-113670000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:113634600-113671200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:113634600-113671600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:113634600-113673000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:113635000-113669600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:113635800-113669800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:113636000-113669800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr1:113636000-113671200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:113636000-113671400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:113636000-113671400	Strong transcription	Fetal Thymus	thymus
23	chr1:113636000-113671600	Strong transcription	Duodenum Mucosa	Duodenum
24	chr1:113636200-113669600	Strong transcription	Fetal Intestine Large	intestine
25	chr1:113636400-113669800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:113636400-113670000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr1:113639200-113669600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:113641200-113669800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:113643600-113670000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:113646400-113672600	Strong transcription	Placenta	Placenta
31	chr1:113650800-113671000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:113651000-113671200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:113653600-113673000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:113655600-113669800	Strong transcription	Hela-S3	cervix
35	chr1:113656600-113669600	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:113656600-113669800	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr1:113656600-113672400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:113656800-113669600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:113656800-113669800	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:113656800-113669800	Strong transcription	Dnd41	blood
41	chr1:113656800-113670000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:113656800-113671600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:113657000-113669600	Strong transcription	Lung	lung
44	chr1:113657000-113669600	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:113657000-113669800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:113657000-113669800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:113657000-113669800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:113657000-113669800	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr1:113657000-113669800	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:113657000-113670000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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