Variant report

Variant	rs369049
Chromosome Location	chr1:220880670-220880671
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	chr1:220862639..220865186-chr1:220879178..220882320,3	K562	blood:

Variant related genes	Relation type
ENSG00000162817	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11118593	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs1690714	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2069044	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2994525	0.80[EUR][1000 genomes]
rs337153	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs337154	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs337172	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs365798	0.90[JPT][hapmap];0.93[YRI][hapmap]
rs381106	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs383681	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3849288	0.83[CEU][hapmap]
rs389499	0.85[AMR][1000 genomes]
rs405196	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs414838	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs416735	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs426020	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs427216	0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs438597	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs442236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7555109	0.83[EUR][1000 genomes]
rs774128	0.84[YRI][hapmap]
rs774132	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs774134	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs774145	0.88[EUR][1000 genomes]
rs774146	0.83[EUR][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
rs369049	MOSC2	cis	Lymphoblastoid	GTEx
rs369049	C1orf115	Cis_1M	lymphoblastoid	RTeQTL
rs369049	C1orf115	cis	Lymphoblastoid	GTEx
rs369049	C1orf115	cis	Nerve Tibial	GTEx
rs369049	MOSC2	Cis_1M	lymphoblastoid	RTeQTL
rs369049	C1orf115	cis	Esophagus Muscularis	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220876600-220881600	Weak transcription	Liver	Liver
2	chr1:220878200-220883800	Enhancers	Fetal Intestine Small	intestine
3	chr1:220878400-220885200	Enhancers	Duodenum Mucosa	Duodenum
4	chr1:220878400-220886000	Enhancers	HepG2	liver
5	chr1:220878800-220885200	Enhancers	Pancreas	Pancrea
6	chr1:220879400-220880800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:220879400-220882600	Weak transcription	Stomach Mucosa	stomach
8	chr1:220879400-220884400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:220879600-220883400	Weak transcription	Adipose Nuclei	Adipose
10	chr1:220880000-220881200	Enhancers	Spleen	Spleen
11	chr1:220880000-220882400	Weak transcription	Right Ventricle	heart
12	chr1:220880000-220882600	Weak transcription	Right Atrium	heart
13	chr1:220880000-220882800	Weak transcription	Left Ventricle	heart
14	chr1:220880200-220881600	Weak transcription	Fetal Intestine Large	intestine
15	chr1:220880200-220882600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:220880400-220883000	Weak transcription	Gastric	stomach
17	chr1:220880400-220883600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:220880600-220881000	Weak transcription	Ovary	ovary
19	chr1:220880600-220882000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:220880600-220882000	Enhancers	Small Intestine	intestine

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