Variant report

Variant	rs427216
Chromosome Location	chr1:220865745-220865746
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	chr1:220862132..220866220-chr1:220920879..220923309,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1690714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337153	0.80[CHD][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs337154	0.80[CHD][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs337191	0.82[AMR][1000 genomes]
rs365798	0.83[TSI][hapmap]
rs366414	0.81[EUR][1000 genomes]
rs369049	0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs381106	0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs383681	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849288	0.82[TSI][hapmap]
rs405196	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs414838	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415273	0.86[AFR][1000 genomes]
rs416735	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426020	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs438597	0.81[JPT][hapmap]
rs442236	0.81[JPT][hapmap]
rs774132	0.81[JPT][hapmap]
rs774138	0.80[EUR][1000 genomes]
rs774145	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs774146	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468194	chr1:220845610-220885612	Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv549227	chr1:220845610-220885612	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2754270	chr1:220850116-220929155	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs427216	C1orf115	cis	lymphoblastoid	seeQTL
rs427216	C1orf115	cis	multi-tissue	Pritchard
rs427216	MOSC2	cis	cerebellum	SCAN
rs427216	C1orf115	cis	Esophagus Muscularis	GTEx
rs427216	MOSC2	cis	lymphoblastoid	seeQTL
rs427216	IARS2	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220863000-220866000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:220863400-220866800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr1:220863600-220866000	Active TSS	Brain Cingulate Gyrus	brain
4	chr1:220863600-220866200	Active TSS	Duodenum Mucosa	Duodenum
5	chr1:220863600-220866200	Active TSS	Fetal Intestine Large	intestine
6	chr1:220863600-220866600	Active TSS	Placenta	Placenta
7	chr1:220864200-220870000	Weak transcription	Aorta	Aorta
8	chr1:220864400-220868400	Weak transcription	Gastric	stomach
9	chr1:220864400-220869800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:220864600-220866000	Flanking Active TSS	Liver	Liver
11	chr1:220864600-220866000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:220864800-220866000	Enhancers	Colon Smooth Muscle	Colon
13	chr1:220865000-220866400	Enhancers	HUVEC	blood vessel
14	chr1:220865000-220870200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:220865000-220870200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:220865200-220866200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:220865200-220866200	Weak transcription	Psoas Muscle	Psoas
18	chr1:220865200-220868400	Weak transcription	Spleen	Spleen
19	chr1:220865200-220870200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:220865200-220873200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:220865200-220874200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:220865200-220879200	Weak transcription	Ovary	ovary
23	chr1:220865400-220866000	Enhancers	HepG2	liver
24	chr1:220865400-220866200	Active TSS	Fetal Intestine Small	intestine
25	chr1:220865400-220868400	Weak transcription	Lung	lung
26	chr1:220865400-220868400	Weak transcription	Pancreas	Pancrea
27	chr1:220865400-220870000	Weak transcription	Left Ventricle	heart
28	chr1:220865400-220870000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:220865400-220870200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:220865400-220870200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:220865400-220870200	Weak transcription	Right Ventricle	heart
32	chr1:220865400-220870800	Weak transcription	Brain Angular Gyrus	brain
33	chr1:220865400-220873200	Weak transcription	Fetal Brain Female	brain
34	chr1:220865400-220873800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:220865400-220874400	Weak transcription	Colonic Mucosa	Colon
36	chr1:220865400-220876200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:220865600-220866000	Weak transcription	Fetal Brain Male	brain
38	chr1:220865600-220867200	Enhancers	Adipose Nuclei	Adipose
39	chr1:220865600-220870200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:220865600-220870800	Weak transcription	Brain Anterior Caudate	brain

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