Variant report

Variant	rs10461973
Chromosome Location	chr5:36705905-36705906
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	chr5:36704160..36706693-chr5:36714837..36716744,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf42-3	chr5:36705782-36705953	ENSG00000250155.1
2	lnc-C5orf42-3	chr5:36705823-36705953	ENSG00000250155.1
3	lnc-C5orf42-3	chr5:36705782-36705955	NONHSAT101040

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10056070	0.87[ASN][1000 genomes]
rs10067333	0.87[ASN][1000 genomes]
rs1025052	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10491377	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10941314	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12658012	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12697368	0.90[ASN][1000 genomes]
rs13178390	0.84[ASN][1000 genomes]
rs1566444	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16903296	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1976377	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2161609	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6451305	0.84[ASN][1000 genomes]
rs6867429	0.85[ASN][1000 genomes]
rs6878201	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6890097	0.85[ASN][1000 genomes]
rs7709455	0.87[ASN][1000 genomes]
rs7734294	0.83[ASN][1000 genomes]
rs919300	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs919301	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs986341	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv830263	chr5:36576504-36755093	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv880571	chr5:36675699-36710205	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10461973	SLC1A3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36700200-36724200	Weak transcription	Primary T cells from cord blood	blood
2	chr5:36701400-36706600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:36701400-36706600	Weak transcription	Spleen	Spleen
4	chr5:36701400-36707000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:36701400-36707400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:36702800-36706000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:36702800-36707400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:36703000-36707400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr5:36703000-36707600	Strong transcription	Primary B cells from cord blood	blood
10	chr5:36703200-36706800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:36703200-36707200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:36703400-36706200	Enhancers	Fetal Muscle Leg	muscle
13	chr5:36703600-36707600	Strong transcription	GM12878-XiMat	blood
14	chr5:36703800-36707400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr5:36704000-36711000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr5:36705400-36711400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:36705800-36706800	Enhancers	Fetal Heart	heart
18	chr5:36705800-36712600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr5:36705800-36724600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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