Variant report

Variant	rs2994990
Chromosome Location	chr1:241666701-241666702
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:241662653..241671177-chr1:241677044..241684165,13	K562	blood:
2	chr1:241665518..241668923-chr1:241674331..241676931,3	MCF-7	breast:
3	chr1:241665859..241668124-chr1:241670823..241673465,2	K562	blood:

Variant related genes	Relation type
ENSG00000091483	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10157091	0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10926494	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2144	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2341935	0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2994981	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2994984	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2994986	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3014576	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3014577	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS 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	40 gene(s)	inside rSNPs	diseases
3	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2994990	RP11-527D7.1	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241655800-241677200	Strong transcription	Liver	Liver
2	chr1:241656400-241666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:241656800-241670000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr1:241656800-241677000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:241656800-241678200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:241657000-241669800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:241657000-241670000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr1:241657000-241675800	Strong transcription	Stomach Smooth Muscle	stomach
9	chr1:241657000-241676000	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr1:241657000-241676200	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:241657000-241676400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:241657000-241677000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:241657000-241677200	Strong transcription	Adipose Nuclei	Adipose
14	chr1:241657000-241677400	Strong transcription	Fetal Thymus	thymus
15	chr1:241657000-241680000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:241657200-241668400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:241657200-241669800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:241657200-241677000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:241657200-241677200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:241657200-241677400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr1:241657400-241676600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr1:241657400-241676800	Strong transcription	K562	blood
23	chr1:241657400-241678600	Strong transcription	Dnd41	blood
24	chr1:241657400-241680000	Strong transcription	Primary B cells from cord blood	blood
25	chr1:241657600-241667800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr1:241657600-241668200	Strong transcription	NH-A	brain
27	chr1:241657600-241672000	Strong transcription	HSMM	muscle
28	chr1:241657600-241676600	Strong transcription	Placenta	Placenta
29	chr1:241657600-241677000	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:241657800-241667800	Strong transcription	Primary hematopoietic stem cells	blood
31	chr1:241657800-241671400	Weak transcription	Stomach Mucosa	stomach
32	chr1:241658200-241671200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr1:241659000-241682000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:241659200-241679800	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:241659600-241679000	Strong transcription	HMEC	breast
36	chr1:241660000-241675800	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:241660200-241666800	Weak transcription	Fetal Heart	heart
38	chr1:241660600-241666800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:241660800-241666800	Weak transcription	Pancreas	Pancrea
40	chr1:241660800-241667000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:241661200-241681400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr1:241661400-241666800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:241662800-241667800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:241662800-241676000	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:241663000-241675200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:241663200-241671000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:241663600-241669400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:241663800-241669800	Strong transcription	Osteobl	bone
49	chr1:241663800-241675800	Strong transcription	Left Ventricle	heart
50	chr1:241663800-241676000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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