Variant report

Variant	rs7544380
Chromosome Location	chr1:151859910-151859911
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151855508..151860878-chr1:151961893..151967107,7	MCF-7	breast:
2	chr1:151857333..151860480-chr1:152007205..152010628,3	MCF-7	breast:
3	chr1:151858557..151860103-chr1:151875689..151877442,2	K562	blood:
4	chr1:151857351..151860092-chr1:151985508..151987866,2	MCF-7	breast:
5	chr1:151858712..151862714-chr1:151863688..151869439,8	K562	blood:
6	chr1:151847463..151849463-chr1:151858810..151860605,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197747	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1003107	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10158030	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1048910	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10749666	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10788813	0.86[EUR][1000 genomes]
rs10788814	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10788816	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10888448	0.85[AMR][1000 genomes]
rs10888449	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10888450	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888451	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888453	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11204905	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11204911	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204912	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1352654	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1490187	0.90[EUR][1000 genomes]
rs1490190	0.85[EUR][1000 genomes]
rs1490191	0.85[ASN][1000 genomes]
rs1552606	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1844542	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1873310	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1873312	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2054948	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2087549	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2130526	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2171917	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2338200	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2338203	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2338204	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2338210	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2932578	0.85[EUR][1000 genomes]
rs2932584	0.83[ASN][1000 genomes]
rs3007682	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3007692	0.83[ASN][1000 genomes]
rs34370890	0.85[ASN][1000 genomes]
rs3748805	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3762427	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4551598	0.92[EUR][1000 genomes]
rs4845385	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4845388	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4845393	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4845660	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845664	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845699	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587626	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6587627	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587628	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587629	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587630	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6659029	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6662463	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6678664	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6685291	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6690443	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6691350	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7529451	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7532721	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7541498	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7545863	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7552869	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs902314	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs902315	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs902316	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9943225	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7544380	THEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151831000-151881400	Weak transcription	Ovary	ovary
2	chr1:151840600-151864600	Weak transcription	NH-A	brain
3	chr1:151841200-151880800	Weak transcription	NHLF	lung
4	chr1:151841400-151860000	Weak transcription	Hela-S3	cervix
5	chr1:151841400-151860200	Weak transcription	Osteobl	bone
6	chr1:151841600-151864000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:151844000-151860000	Weak transcription	HSMM	muscle
8	chr1:151844000-151864600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:151844200-151860400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:151844400-151866400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:151844400-151881200	Weak transcription	Aorta	Aorta
12	chr1:151844600-151863600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:151844600-151864200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:151844800-151863800	Weak transcription	Brain Substantia Nigra	brain
15	chr1:151844800-151864200	Weak transcription	Pancreas	Pancrea
16	chr1:151844800-151870800	Weak transcription	Gastric	stomach
17	chr1:151844800-151871200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:151844800-151877600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:151845200-151863600	Weak transcription	Fetal Kidney	kidney
20	chr1:151845400-151871200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:151846000-151861800	Weak transcription	Psoas Muscle	Psoas
22	chr1:151846000-151864200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:151846400-151860000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:151846400-151860200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:151846400-151865400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:151846400-151870400	Weak transcription	Right Ventricle	heart
27	chr1:151846400-151871600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:151846600-151864800	Weak transcription	Fetal Lung	lung
29	chr1:151846800-151860400	Weak transcription	Brain Anterior Caudate	brain
30	chr1:151846800-151860400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:151846800-151860600	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:151846800-151863000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:151847000-151863800	Weak transcription	Fetal Thymus	thymus
34	chr1:151847000-151865000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:151847000-151869600	Weak transcription	Small Intestine	intestine
36	chr1:151847000-151871000	Weak transcription	Spleen	Spleen
37	chr1:151847200-151860200	Weak transcription	Lung	lung
38	chr1:151847400-151860000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:151847400-151860200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:151847400-151870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:151847600-151862000	Weak transcription	Adipose Nuclei	Adipose
42	chr1:151847800-151864000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:151848000-151860000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:151848000-151863000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:151848400-151860200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:151848400-151863600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:151848800-151860000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:151848800-151860000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:151850000-151860000	Weak transcription	Primary T cells from cord blood	blood
50	chr1:151850800-151860200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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