Variant report

Variant	rs2383477
Chromosome Location	chr1:186351104-186351105
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	chr1:186350456..186352383-chr1:186365203..186367027,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268662	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10798041	0.82[CHB][hapmap];0.80[GIH][hapmap]
rs10911861	0.82[CHB][hapmap];0.80[GIH][hapmap]
rs10911864	0.82[CHB][hapmap]
rs10911866	0.82[CHB][hapmap]
rs10911886	0.82[CHB][hapmap]
rs12057695	0.82[CHB][hapmap]
rs12081510	1.00[CHB][hapmap]
rs12407957	0.82[CHB][hapmap];0.80[GIH][hapmap]
rs1882926	0.82[CHB][hapmap];0.80[GIH][hapmap]
rs1929095	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs2178214	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2891247	0.82[CHB][hapmap]
rs35066734	0.82[CHB][hapmap];0.80[GIH][hapmap]
rs6672638	0.82[CHB][hapmap];0.80[GIH][hapmap]
rs7512750	0.82[CHB][hapmap];0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv548399	chr1:186295930-186353461	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
4	esv1822818	chr1:186301447-186441585	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2383477	SMG7	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186345400-186358000	Weak transcription	Left Ventricle	heart
2	chr1:186345400-186358600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:186345400-186359000	Weak transcription	Lung	lung
4	chr1:186345400-186371600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:186345400-186371600	Weak transcription	Esophagus	oesophagus
6	chr1:186345400-186371600	Weak transcription	Gastric	stomach
7	chr1:186345400-186390600	Weak transcription	Small Intestine	intestine
8	chr1:186345400-186398200	Weak transcription	Spleen	Spleen
9	chr1:186345800-186361200	Weak transcription	Aorta	Aorta
10	chr1:186345800-186377400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:186346000-186353200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:186346000-186366800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:186346200-186351400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:186346200-186351800	Weak transcription	Fetal Lung	lung
15	chr1:186346200-186357400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:186346200-186357800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:186346200-186357800	Weak transcription	Brain Anterior Caudate	brain
18	chr1:186346200-186357800	Weak transcription	Fetal Kidney	kidney
19	chr1:186346200-186359000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:186346200-186359000	Weak transcription	Ovary	ovary
21	chr1:186346200-186359000	Weak transcription	Thymus	Thymus
22	chr1:186346200-186360600	Weak transcription	Brain Substantia Nigra	brain
23	chr1:186346200-186361200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:186346200-186361200	Weak transcription	Pancreas	Pancrea
25	chr1:186346200-186361400	Weak transcription	Right Ventricle	heart
26	chr1:186346200-186365200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:186346200-186365200	Weak transcription	Psoas Muscle	Psoas
28	chr1:186346200-186380400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:186346200-186388400	Weak transcription	Colonic Mucosa	Colon
30	chr1:186346400-186351200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:186346400-186351800	Weak transcription	Fetal Brain Male	brain
32	chr1:186346400-186351800	Weak transcription	A549	lung
33	chr1:186346400-186352000	Weak transcription	Brain Germinal Matrix	brain
34	chr1:186346400-186352200	Weak transcription	HMEC	breast
35	chr1:186346400-186354400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:186346400-186357800	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:186346400-186359400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:186346400-186359400	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:186346400-186361000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr1:186346400-186361200	Weak transcription	Brain Angular Gyrus	brain
41	chr1:186346400-186376000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr1:186346400-186388000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:186346400-186390000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:186346600-186357400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:186346600-186357400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:186346600-186359400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr1:186346800-186352000	Weak transcription	Fetal Brain Female	brain
48	chr1:186346800-186354000	Weak transcription	Fetal Heart	heart
49	chr1:186346800-186354600	Strong transcription	K562	blood
50	chr1:186346800-186357400	Weak transcription	Stomach Mucosa	stomach

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