Variant report

Variant	rs1220394
Chromosome Location	chr1:9909506-9909507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9882501..9887964-chr1:9906388..9911794,10	MCF-7	breast:
2	chr1:9882289..9884339-chr1:9907801..9910859,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMNAT1-3	chr1:9909427-9909532	ENSG00000223989.1
2	lnc-NMNAT1-3	chr1:9909113-9910860	NONHSAT000821

Variant related genes	Relation type
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1220382	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220383	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1220384	0.81[EUR][1000 genomes]
rs1220391	0.85[ASN][1000 genomes]
rs1220392	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1220393	0.94[EUR][1000 genomes]
rs1220395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220396	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1220404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1220405	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1220406	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220409	0.96[ASN][1000 genomes]
rs1220411	0.87[EUR][1000 genomes]
rs1220412	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1220413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1220418	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1372106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1470160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1660735	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2083577	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2379108	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2486084	0.82[EUR][1000 genomes]
rs2582980	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2582981	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3120822	0.83[EUR][1000 genomes]
rs7225	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935073	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs935074	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs935075	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs946275	1.00[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv871146	chr1:9897001-9951288	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9896000-9919200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:9896600-9913400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:9902200-9909800	Enhancers	Fetal Thymus	thymus
4	chr1:9902600-9911800	Weak transcription	HSMM	muscle
5	chr1:9902800-9913600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:9903200-9912200	Weak transcription	HSMMtube	muscle
7	chr1:9904000-9909800	Weak transcription	HepG2	liver
8	chr1:9904000-9913000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:9904000-9929800	Weak transcription	Aorta	Aorta
10	chr1:9904200-9910400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:9904200-9912400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:9904200-9927400	Weak transcription	Colonic Mucosa	Colon
13	chr1:9904200-9927800	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:9904400-9911800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:9904400-9913400	Weak transcription	Fetal Lung	lung
16	chr1:9904400-9922600	Weak transcription	Pancreas	Pancrea
17	chr1:9904400-9923400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:9904400-9927800	Weak transcription	Stomach Mucosa	stomach
19	chr1:9904400-9930000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:9904600-9922600	Weak transcription	Ovary	ovary
21	chr1:9904600-9935000	Weak transcription	Osteobl	bone
22	chr1:9904800-9910800	Weak transcription	Fetal Brain Female	brain
23	chr1:9904800-9946000	Weak transcription	Fetal Kidney	kidney
24	chr1:9905000-9909600	Weak transcription	Fetal Brain Male	brain
25	chr1:9905000-9911800	Weak transcription	HMEC	breast
26	chr1:9905200-9915400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:9905600-9909600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr1:9906200-9910200	Enhancers	Primary hematopoietic stem cells	blood
29	chr1:9906200-9912400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr1:9906600-9927400	Weak transcription	Liver	Liver
31	chr1:9906800-9910200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:9906800-9910800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:9907000-9912000	Strong transcription	NHEK	skin
34	chr1:9907000-9913000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:9907000-9913400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:9907000-9919200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:9907000-9930000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:9907200-9910600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:9907200-9910800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:9907200-9911200	Enhancers	Fetal Heart	heart
41	chr1:9907200-9912000	Weak transcription	Brain Substantia Nigra	brain
42	chr1:9907400-9910000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:9907400-9910600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:9907400-9910800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr1:9907400-9910800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:9907400-9910800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:9907400-9910800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:9907400-9913600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:9907400-9914200	Strong transcription	Adipose Nuclei	Adipose
50	chr1:9907400-9929800	Weak transcription	Rectal Smooth Muscle	rectum

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