Variant report

Variant	rs12278318
Chromosome Location	chr11:34876507-34876508
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	chr11:34868671..34870522-chr11:34876282..34878999,2	MCF-7	breast:
2	chr11:34875503..34877981-chr11:34878649..34881731,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ELF5-3	chr11:34876500-34876870	NONHSAT018762

Extended variants
information (count: 94 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10488805	1.00[ASN][1000 genomes]
rs1049333	0.90[ASN][1000 genomes]
rs10836316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10836317	0.86[EUR][1000 genomes]
rs11032891	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032894	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032895	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032898	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032899	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032907	0.83[ASN][1000 genomes]
rs11032939	1.00[ASN][1000 genomes]
rs11032956	1.00[ASN][1000 genomes]
rs11032958	1.00[ASN][1000 genomes]
rs11032959	1.00[ASN][1000 genomes]
rs11032960	1.00[ASN][1000 genomes]
rs11032961	1.00[ASN][1000 genomes]
rs11032963	1.00[ASN][1000 genomes]
rs11032970	1.00[ASN][1000 genomes]
rs11602364	0.83[EUR][1000 genomes]
rs11607986	0.86[EUR][1000 genomes]
rs12271867	1.00[ASN][1000 genomes]
rs12272820	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12273167	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12274680	1.00[ASN][1000 genomes]
rs12276679	1.00[ASN][1000 genomes]
rs12279952	1.00[ASN][1000 genomes]
rs12280958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12284844	1.00[ASN][1000 genomes]
rs12290759	1.00[ASN][1000 genomes]
rs12291039	1.00[ASN][1000 genomes]
rs12292931	1.00[ASN][1000 genomes]
rs12292993	1.00[ASN][1000 genomes]
rs12294339	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12294397	1.00[ASN][1000 genomes]
rs1509659	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509660	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16926365	1.00[ASN][1000 genomes]
rs16926479	1.00[ASN][1000 genomes]
rs16926673	0.90[ASN][1000 genomes]
rs17362114	1.00[ASN][1000 genomes]
rs17364197	0.90[ASN][1000 genomes]
rs17436343	0.90[ASN][1000 genomes]
rs17711539	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17712273	1.00[ASN][1000 genomes]
rs17783998	0.83[EUR][1000 genomes]
rs17784324	0.88[EUR][1000 genomes]
rs1828299	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077926	0.83[ASN][1000 genomes]
rs41512444	1.00[ASN][1000 genomes]
rs4534556	0.87[EUR][1000 genomes]
rs55796371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55911702	0.87[EUR][1000 genomes]
rs56061305	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56922113	1.00[ASN][1000 genomes]
rs57611620	1.00[ASN][1000 genomes]
rs58127349	1.00[ASN][1000 genomes]
rs59676516	1.00[ASN][1000 genomes]
rs61760973	1.00[ASN][1000 genomes]
rs61882175	1.00[ASN][1000 genomes]
rs6484738	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114359	1.00[ASN][1000 genomes]
rs7114970	0.91[ASN][1000 genomes]
rs7115217	1.00[ASN][1000 genomes]
rs7115749	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119807	1.00[ASN][1000 genomes]
rs7120509	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7122048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7124099	1.00[ASN][1000 genomes]
rs7124428	1.00[ASN][1000 genomes]
rs7129517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130678	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130774	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131229	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131272	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72922479	0.83[EUR][1000 genomes]
rs72922482	0.83[EUR][1000 genomes]
rs72924508	0.88[EUR][1000 genomes]
rs7924969	1.00[ASN][1000 genomes]
rs7927857	1.00[ASN][1000 genomes]
rs7929287	1.00[ASN][1000 genomes]
rs7932461	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7936426	1.00[ASN][1000 genomes]
rs7936983	1.00[ASN][1000 genomes]
rs7937316	0.84[EUR][1000 genomes]
rs7941937	1.00[ASN][1000 genomes]
rs7945524	1.00[ASN][1000 genomes]
rs7947848	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832118	chr11:34743123-34903951	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv832119	chr11:34815528-35009370	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12278318	APIP	cis	Thyroid	GTEx
rs12278318	APIP	cis	Esophagus Muscularis	GTEx
rs12278318	APIP	cis	Artery Tibial	GTEx
rs12278318	APIP	cis	Heart Left Ventricle	GTEx
rs12278318	APIP	cis	Skin Sun Exposed Lower leg	GTEx
rs12278318	APIP	cis	Nerve Tibial	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34859000-34909400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:34872200-34886600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:34872800-34876600	Weak transcription	Hela-S3	cervix
4	chr11:34875200-34877200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr11:34875400-34877800	Enhancers	Stomach Mucosa	stomach
6	chr11:34875600-34876800	Enhancers	Duodenum Mucosa	Duodenum
7	chr11:34875600-34877400	Enhancers	Fetal Intestine Large	intestine
8	chr11:34875600-34877400	Enhancers	Fetal Intestine Small	intestine
9	chr11:34875800-34877400	Enhancers	Psoas Muscle	Psoas
10	chr11:34876000-34877400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:34876200-34876600	Weak transcription	Esophagus	oesophagus
12	chr11:34876200-34877200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr11:34876200-34878200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:34876200-34878200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr11:34876400-34876600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:34876400-34877000	Enhancers	A549	lung
17	chr11:34876400-34877200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr11:34876400-34877600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr11:34876400-34878800	Weak transcription	Small Intestine	intestine

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