Variant report

Variant	rs861578
Chromosome Location	chr1:184729032-184729033
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184722577..184724889-chr1:184727067..184730117,4	MCF-7	breast:
2	chr1:184728189..184730615-chr1:184744000..184745636,2	MCF-7	breast:
3	chr1:184722946..184726170-chr1:184728619..184730766,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf21-7	chr1:184727266-184730133	NONHSAT008399

Variant related genes	Relation type
ENSG00000116406	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1061508	0.91[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10911644	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs10911645	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12032144	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12071631	0.91[GIH][hapmap]
rs12124714	0.97[ASN][1000 genomes]
rs12124929	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs12131285	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12567225	0.95[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs12567226	0.95[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs2024764	0.90[ASN][1000 genomes]
rs2024766	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2024767	0.91[GIH][hapmap]
rs2064605	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2333715	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs2333716	0.88[GIH][hapmap]
rs35478695	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35779894	0.81[YRI][hapmap]
rs3736757	0.91[GIH][hapmap]
rs3895196	1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4651230	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs6663178	0.89[GIH][hapmap]
rs726427	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs861575	0.84[GIH][hapmap]
rs861579	0.91[EUR][1000 genomes]
rs861581	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs861582	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9425343	0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs9425634	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9425635	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs971080	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9787132	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1009529	chr1:184663898-184731215	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs861578	OCLM	cis	parietal	SCAN
rs861578	FAM129A	cis	cerebellum	SCAN
rs861578	EDEM3	cis	Esophagus Muscularis	GTEx
rs861578	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs861578	PRG4	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184724800-184742600	Weak transcription	Gastric	stomach
2	chr1:184725200-184731200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:184725400-184730000	Enhancers	Stomach Mucosa	stomach
4	chr1:184728000-184729600	Enhancers	HepG2	liver
5	chr1:184728200-184729200	Enhancers	HSMM	muscle
6	chr1:184728200-184730000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:184728400-184729400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:184728400-184729400	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr1:184728400-184729400	Enhancers	A549	lung
10	chr1:184728400-184729600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr1:184728600-184729200	Enhancers	Fetal Intestine Small	intestine
12	chr1:184728600-184729400	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr1:184728800-184729400	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:184728800-184729400	Enhancers	HSMMtube	muscle
15	chr1:184728800-184731200	Weak transcription	Liver	Liver
16	chr1:184729000-184729400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr1:184729000-184729600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr1:184729000-184730000	Enhancers	Pancreas	Pancrea

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