Variant report

Variant	rs73013957
Chromosome Location	chr3:156378570-156378571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156371088..156373654-chr3:156376805..156378893,2	K562	blood:
2	chr3:156376696..156378719-chr3:156391982..156394592,2	MCF-7	breast:
3	chr3:156377079..156379353-chr3:156380561..156383322,2	K562	blood:
4	chr3:156377877..156380030-chr3:156386212..156388367,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSR3-7	chr3:156359231-156383752	predAs_chen_BG181400_1

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10513495	0.87[EUR][1000 genomes]
rs12636629	0.80[EUR][1000 genomes]
rs1367312	0.93[EUR][1000 genomes]
rs1529581	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17373227	0.92[EUR][1000 genomes]
rs41366145	0.80[EUR][1000 genomes]
rs4364127	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55686038	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56128116	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56152727	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56245561	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56354026	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56357051	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56836190	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56960846	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57483705	0.80[EUR][1000 genomes]
rs58263861	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58822703	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59689193	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60032002	0.82[ASN][1000 genomes]
rs60178381	1.00[ASN][1000 genomes]
rs73012038	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73012046	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73019737	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73019748	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73019749	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891463	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs919520	0.87[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	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv3412943	chr3:156377208-156379406	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs73013957	LINC00886	cis	Thyroid	GTEx
rs73013957	LINC00886	cis	Artery Tibial	GTEx
rs73013957	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156375000-156378600	Weak transcription	GM12878-XiMat	blood
2	chr3:156375600-156381800	Weak transcription	K562	blood
3	chr3:156376600-156382400	Weak transcription	Fetal Kidney	kidney
4	chr3:156376600-156383800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:156376600-156385600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:156377400-156381600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:156377400-156382200	Weak transcription	HSMMtube	muscle
8	chr3:156377400-156386000	Weak transcription	Psoas Muscle	Psoas
9	chr3:156377600-156382200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:156377600-156382200	Weak transcription	Brain Germinal Matrix	brain
11	chr3:156377600-156383000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:156378400-156379000	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr3:156378400-156380000	Enhancers	Primary B cells from peripheral blood	blood
14	chr3:156378400-156380200	Enhancers	Primary monocytes fromperipheralblood	blood

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