Variant report

Variant	rs7512209
Chromosome Location	chr1:228311716-228311717
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228308851..228311913-chr1:228318385..228321498,4	K562	blood:
2	chr1:228306052..228307610-chr1:228310727..228312668,2	K562	blood:
3	chr1:228269694..228271552-chr1:228310109..228312987,2	K562	blood:
4	chr1:228295648..228299640-chr1:228308669..228311960,3	K562	blood:
5	chr1:228296008..228299455-chr1:228310076..228314109,6	MCF-7	breast:
6	chr1:228309213..228312367-chr1:228313234..228315768,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GUK1-2	chr1:228306596-228311865	NONHSAT009977

No data

Variant related genes	Relation type
ENSG00000162910	Chromatin interaction
ENSG00000143761	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10158357	0.84[CEU][hapmap]
rs1059778	1.00[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs10753445	1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs10799468	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10799471	0.81[EUR][1000 genomes]
rs10916265	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10916268	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916271	0.90[EUR][1000 genomes]
rs11584385	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs11799681	0.81[EUR][1000 genomes]
rs11804508	0.82[EUR][1000 genomes]
rs12024649	0.81[EUR][1000 genomes]
rs12084338	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs12118872	0.91[CEU][hapmap]
rs12130630	0.84[CEU][hapmap]
rs12134624	0.92[TSI][hapmap]
rs12564763	0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12726781	0.82[EUR][1000 genomes]
rs12745416	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1411910	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs1557026	0.84[CEU][hapmap]
rs1620111	1.00[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs1629294	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap]
rs1745417	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1745423	0.87[TSI][hapmap]
rs1757132	1.00[CEU][hapmap]
rs1757133	1.00[CEU][hapmap]
rs1757139	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap]
rs1757147	1.00[CEU][hapmap]
rs1757149	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap]
rs1757150	1.00[CEU][hapmap]
rs1757152	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.88[TSI][hapmap]
rs1757156	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap]
rs17640616	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs1771459	1.00[CEU][hapmap];0.80[GIH][hapmap]
rs1771460	0.88[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap]
rs1771461	1.00[CEU][hapmap]
rs1771462	1.00[CEU][hapmap]
rs1771467	1.00[CEU][hapmap]
rs1771472	1.00[CEU][hapmap]
rs1771474	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap]
rs1771476	1.00[CEU][hapmap]
rs1771479	1.00[CEU][hapmap]
rs1771482	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs1771483	1.00[CEU][hapmap]
rs1771484	0.96[CEU][hapmap]
rs1771485	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs1771487	0.96[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1832734	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2066237	1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap]
rs2185544	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2313601	1.00[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs2313602	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2776853	0.82[EUR][1000 genomes]
rs2776855	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs2776856	0.88[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap]
rs2872538	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs3094912	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs3094913	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs3094914	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs3121191	0.80[EUR][1000 genomes]
rs3121192	0.81[EUR][1000 genomes]
rs3795782	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs4653536	0.92[EUR][1000 genomes]
rs4653915	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs4653917	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs4653921	0.84[CEU][hapmap]
rs493945	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs55971985	0.82[EUR][1000 genomes]
rs6426492	0.81[CEU][hapmap]
rs6657968	0.84[CEU][hapmap]
rs6673893	0.84[CEU][hapmap]
rs6682260	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs708111	0.85[CHB][hapmap]
rs708112	0.86[CHB][hapmap]
rs708114	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs708118	0.82[YRI][hapmap]
rs7532924	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7537636	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539762	0.84[CEU][hapmap];0.92[TSI][hapmap]
rs849749	0.85[TSI][hapmap]
rs947087	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs964941	0.86[CHB][hapmap];0.82[YRI][hapmap]

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	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
4	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
5	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
7	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	91 gene(s)	inside rSNPs	diseases
9	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7512209	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs7512209	IBA57	cis	Whole Blood	GTEx
rs7512209	WDR26	cis	cerebellum	SCAN
rs7512209	MRPL55	cis	cerebellum	SCAN
rs7512209	OBSCN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228309200-228314000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:228309400-228313000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:228309600-228314200	Enhancers	Fetal Intestine Small	intestine
4	chr1:228309800-228314200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:228310000-228313400	Enhancers	Fetal Intestine Large	intestine
6	chr1:228310400-228312000	Enhancers	K562	blood
7	chr1:228311000-228312400	Enhancers	HepG2	liver
8	chr1:228311400-228312400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:228311600-228313200	Enhancers	Duodenum Mucosa	Duodenum

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