Variant report

Variant	rs946273
Chromosome Location	chr1:9908515-9908516
allele	A/G
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	chr1:9908376-9908524	ENSG00000223989.1
2	lnc-NMNAT1-3	chr1:9908341-9908911	NONHSAT000821

Variant related genes	Relation type
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12066330	1.00[EUR][1000 genomes]
rs1220388	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1220403	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1220407	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6679984	1.00[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	chr1:9896400-9908800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:9896600-9913400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:9902000-9908600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:9902200-9909800	Enhancers	Fetal Thymus	thymus
6	chr1:9902600-9911800	Weak transcription	HSMM	muscle
7	chr1:9902800-9913600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:9903200-9912200	Weak transcription	HSMMtube	muscle
9	chr1:9904000-9909400	Weak transcription	Gastric	stomach
10	chr1:9904000-9909800	Weak transcription	HepG2	liver
11	chr1:9904000-9913000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:9904000-9929800	Weak transcription	Aorta	Aorta
13	chr1:9904200-9910400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:9904200-9912400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:9904200-9927400	Weak transcription	Colonic Mucosa	Colon
16	chr1:9904200-9927800	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:9904400-9909200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:9904400-9909400	Weak transcription	Brain Germinal Matrix	brain
19	chr1:9904400-9911800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:9904400-9913400	Weak transcription	Fetal Lung	lung
21	chr1:9904400-9922600	Weak transcription	Pancreas	Pancrea
22	chr1:9904400-9923400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:9904400-9927800	Weak transcription	Stomach Mucosa	stomach
24	chr1:9904400-9930000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:9904600-9922600	Weak transcription	Ovary	ovary
26	chr1:9904600-9935000	Weak transcription	Osteobl	bone
27	chr1:9904800-9908800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:9904800-9910800	Weak transcription	Fetal Brain Female	brain
29	chr1:9904800-9946000	Weak transcription	Fetal Kidney	kidney
30	chr1:9905000-9909600	Weak transcription	Fetal Brain Male	brain
31	chr1:9905000-9911800	Weak transcription	HMEC	breast
32	chr1:9905200-9915400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:9905400-9908800	Enhancers	K562	blood
34	chr1:9905600-9909200	Weak transcription	NHLF	lung
35	chr1:9905600-9909600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr1:9906000-9909400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:9906200-9910200	Enhancers	Primary hematopoietic stem cells	blood
38	chr1:9906200-9912400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:9906600-9909200	Weak transcription	Placenta	Placenta
40	chr1:9906600-9927400	Weak transcription	Liver	Liver
41	chr1:9906800-9910200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:9906800-9910800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr1:9907000-9908600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:9907000-9909000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr1:9907000-9912000	Strong transcription	NHEK	skin
46	chr1:9907000-9913000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:9907000-9913400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:9907000-9919200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:9907000-9930000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:9907200-9908600	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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