Variant report

Variant	rs638877
Chromosome Location	chr1:228130579-228130580
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228128193..228132003-chr1:228132864..228136285,5	K562	blood:
2	chr1:227949872..227950667-chr1:228129639..228130594,3	MCF-7	breast:
3	chr1:227921810..227924272-chr1:228130209..228131877,2	MCF-7	breast:
4	chr1:227948596..227951213-chr1:228129640..228131293,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143740	Chromatin interaction
ENSG00000081692	Chromatin interaction
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11584326	0.85[EUR][1000 genomes]
rs1418422	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1636193	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1636194	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1774754	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2262292	0.84[EUR][1000 genomes]
rs2313118	0.81[AFR][1000 genomes]
rs2485254	0.97[EUR][1000 genomes]
rs2527614	0.84[AFR][1000 genomes]
rs2796055	0.97[EUR][1000 genomes]
rs587000	0.97[EUR][1000 genomes]
rs590657	0.82[AFR][1000 genomes]
rs594916	0.81[AFR][1000 genomes]
rs601050	0.84[EUR][1000 genomes]
rs631768	0.83[AFR][1000 genomes]
rs640440	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs652141	0.91[EUR][1000 genomes]
rs662658	0.96[EUR][1000 genomes]
rs680148	0.97[EUR][1000 genomes]
rs681824	0.96[EUR][1000 genomes]
rs849900	0.96[EUR][1000 genomes]
rs849904	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
9	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs638877	OBSCN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228107800-228134400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:228109600-228132000	Weak transcription	Gastric	stomach
3	chr1:228109800-228134000	Weak transcription	Right Atrium	heart
4	chr1:228118400-228133000	Weak transcription	Ovary	ovary
5	chr1:228121000-228132600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:228123800-228132000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:228123800-228132600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:228125600-228130800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:228126000-228130800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:228126200-228134400	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr1:228126600-228133400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr1:228127000-228133600	Enhancers	Fetal Muscle Leg	muscle
13	chr1:228128000-228133400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:228128200-228131600	Enhancers	Right Ventricle	heart
15	chr1:228128200-228132800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:228128400-228132200	Weak transcription	Esophagus	oesophagus
17	chr1:228128400-228133600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:228128800-228131000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr1:228128800-228132200	Weak transcription	HMEC	breast
20	chr1:228129000-228132800	Weak transcription	HSMM	muscle
21	chr1:228129200-228131000	Enhancers	Fetal Heart	heart
22	chr1:228129400-228131200	Weak transcription	Fetal Intestine Large	intestine
23	chr1:228129400-228132000	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr1:228129400-228134400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr1:228129600-228130800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:228129800-228130600	Enhancers	HSMMtube	muscle
27	chr1:228130000-228131200	Active TSS	Psoas Muscle	Psoas
28	chr1:228130000-228131800	Flanking Active TSS	Rectal Smooth Muscle	rectum
29	chr1:228130200-228130600	Weak transcription	Brain Substantia Nigra	brain
30	chr1:228130200-228130600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:228130200-228131400	Flanking Active TSS	Fetal Stomach	stomach
32	chr1:228130200-228132200	Weak transcription	Pancreas	Pancrea
33	chr1:228130200-228132200	Weak transcription	Spleen	Spleen
34	chr1:228130200-228133000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:228130200-228133600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr1:228130400-228131200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:228130400-228131800	Weak transcription	Fetal Lung	lung
38	chr1:228130400-228133000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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