Variant report

Variant	rs438597
Chromosome Location	chr1:220878259-220878260
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220799540..220802603-chr1:220876987..220879444,3	K562	blood:

Variant related genes	Relation type
ENSG00000233012	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11118593	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs1690714	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2069044	0.84[CEU][hapmap]
rs337153	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs337154	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs337172	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs365798	0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap]
rs369049	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]
rs381106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs383681	0.89[AMR][1000 genomes];0.91[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];0.93[EUR][1000 genomes]
rs414838	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs416735	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs426020	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs427216	0.81[JPT][hapmap]
rs442236	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7555109	0.82[EUR][1000 genomes]
rs774128	0.85[YRI][hapmap]
rs774132	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774134	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs774145	0.87[EUR][1000 genomes]
rs774146	0.82[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs438597	C1orf115	cis	Lymphoblastoid	GTEx
rs438597	C1orf115	Cis_1M	lymphoblastoid	RTeQTL
rs438597	MOSC2	Cis_1M	lymphoblastoid	RTeQTL
rs438597	C1orf115	cis	Esophagus Muscularis	GTEx
rs438597	MOSC2	cis	Lymphoblastoid	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220865200-220879200	Weak transcription	Ovary	ovary
2	chr1:220866600-220879600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:220871600-220878400	Weak transcription	Gastric	stomach
4	chr1:220871800-220878800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:220872200-220878800	Weak transcription	Fetal Intestine Large	intestine
6	chr1:220873400-220878800	Weak transcription	Pancreas	Pancrea
7	chr1:220873600-220879400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:220873800-220878400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:220873800-220878400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:220873800-220880000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:220874400-220879200	Weak transcription	Placenta	Placenta
12	chr1:220876400-220878400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:220876600-220881600	Weak transcription	Liver	Liver
14	chr1:220876800-220878600	Weak transcription	Right Atrium	heart
15	chr1:220876800-220878600	Weak transcription	Stomach Mucosa	stomach
16	chr1:220876800-220879200	Weak transcription	Adipose Nuclei	Adipose
17	chr1:220876800-220879400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:220876800-220879600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:220877200-220878400	Weak transcription	HepG2	liver
20	chr1:220877200-220879400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:220877200-220879800	Weak transcription	Small Intestine	intestine
22	chr1:220877400-220878400	Weak transcription	Spleen	Spleen
23	chr1:220877400-220878800	Weak transcription	Right Ventricle	heart
24	chr1:220877400-220879400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:220877400-220880200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:220878200-220880000	Enhancers	Fetal Heart	heart
27	chr1:220878200-220880000	Enhancers	Left Ventricle	heart
28	chr1:220878200-220883800	Enhancers	Fetal Intestine Small	intestine

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