Variant report

Variant	rs1873310
Chromosome Location	chr1:151837283-151837284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151833646..151837340-chr1:151842785..151845741,4	MCF-7	breast:
2	chr1:151832360..151835660-chr1:151836036..151839920,4	MCF-7	breast:
3	chr1:151836666..151838298-chr1:151846377..151848819,2	MCF-7	breast:
4	chr1:151811898..151813917-chr1:151836689..151839766,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225556	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1003107	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10158030	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1038746	1.00[CHB][hapmap]
rs1038748	1.00[CHB][hapmap]
rs1048910	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10749666	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10788813	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10788814	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10788816	1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10888448	0.83[AMR][1000 genomes]
rs10888449	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10888450	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10888451	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10888453	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11204905	0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11204911	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11204912	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11204923	1.00[CHB][hapmap]
rs12723616	1.00[CHB][hapmap]
rs1352654	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1490187	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490190	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1552605	0.83[YRI][hapmap]
rs1552606	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1552607	1.00[CHB][hapmap]
rs1602245	1.00[CHB][hapmap]
rs1602248	1.00[CHB][hapmap]
rs17583707	1.00[CHB][hapmap]
rs1844542	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1873311	1.00[CHB][hapmap]
rs1873312	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1967085	1.00[CHB][hapmap]
rs2054948	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2087549	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2130526	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2171917	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2338018	1.00[CHB][hapmap]
rs2338200	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2338203	1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2338204	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2338210	0.84[AMR][1000 genomes]
rs2932563	1.00[CHB][hapmap]
rs2932567	1.00[CHB][hapmap]
rs2932578	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2932592	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs2999514	1.00[CHB][hapmap]
rs2999527	1.00[CHB][hapmap]
rs2999536	1.00[CHB][hapmap]
rs2999552	1.00[CHB][hapmap]
rs2999558	1.00[CHB][hapmap]
rs3007682	0.82[AMR][1000 genomes]
rs3007701	1.00[CHB][hapmap]
rs3748805	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3762427	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4551598	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845388	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4845393	1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4845660	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4845664	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4845699	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6587626	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587627	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6587628	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6587629	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587630	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6659029	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6662463	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6678664	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6685291	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6690443	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6691350	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7529451	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7532721	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7541498	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7544380	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7545863	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7552869	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902314	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs902315	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs902316	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9943225	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008033	chr1:151785029-151843154	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1873310	THEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151819200-151847600	Weak transcription	Thymus	Thymus
2	chr1:151821600-151845600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:151826400-151846200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:151827600-151839800	Weak transcription	Hela-S3	cervix
5	chr1:151829000-151845200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:151831000-151881400	Weak transcription	Ovary	ovary
7	chr1:151832000-151859600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:151832800-151840000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:151832800-151846000	Weak transcription	Spleen	Spleen
10	chr1:151833400-151840200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:151833600-151837400	Weak transcription	Fetal Thymus	thymus
12	chr1:151833800-151840400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:151834000-151849600	Weak transcription	Esophagus	oesophagus
14	chr1:151834600-151839200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr1:151835000-151839000	Weak transcription	Placenta	Placenta
16	chr1:151835400-151838800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr1:151835600-151847600	Weak transcription	HSMMtube	muscle
18	chr1:151836600-151837400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:151836800-151837800	Enhancers	Adipose Nuclei	Adipose
20	chr1:151837000-151837600	Enhancers	Right Ventricle	heart
21	chr1:151837200-151837400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:151837200-151837400	Enhancers	Left Ventricle	heart
23	chr1:151837200-151837600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr1:151837200-151840400	Weak transcription	Fetal Lung	lung
25	chr1:151837200-151845600	Weak transcription	Lung	lung

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