Variant report

Variant	rs2054948
Chromosome Location	chr1:151875388-151875389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151867613..151869663-chr1:151873310..151875520,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1003107	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158030	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1048910	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749666	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10788813	0.81[EUR][1000 genomes]
rs10788814	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10788816	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888448	0.85[AMR][1000 genomes]
rs10888449	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888450	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10888451	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10888453	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204905	0.95[AMR][1000 genomes]
rs11204911	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11204912	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1352654	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1490187	0.84[EUR][1000 genomes]
rs1490190	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1552606	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17583707	0.85[ASN][1000 genomes]
rs1844542	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1873310	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1873312	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087549	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2130526	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171917	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2338200	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2338203	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2338204	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2338210	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2932578	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007682	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3748805	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762427	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4551598	0.83[EUR][1000 genomes]
rs4845385	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4845388	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845393	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845660	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4845664	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4845699	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61113720	0.85[ASN][1000 genomes]
rs6587626	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6587627	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6587628	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6587629	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587630	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6659029	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6662463	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678664	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6685291	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6690443	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691350	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529451	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7532721	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7541498	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7544380	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7545863	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7552869	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs902314	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs902315	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs902316	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9943225	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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
rs2054948	THEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151831000-151881400	Weak transcription	Ovary	ovary
2	chr1:151841200-151880800	Weak transcription	NHLF	lung
3	chr1:151844400-151881200	Weak transcription	Aorta	Aorta
4	chr1:151844800-151877600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:151854000-151880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:151860600-151877600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:151860800-151879800	Weak transcription	Brain Angular Gyrus	brain
8	chr1:151861600-151879800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:151862400-151880400	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:151864800-151881400	Weak transcription	Brain Substantia Nigra	brain
11	chr1:151866200-151879600	Weak transcription	NHDF-Ad	bronchial
12	chr1:151866200-151880200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:151866600-151879800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:151867200-151879600	Weak transcription	Fetal Stomach	stomach
15	chr1:151867400-151877600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:151867400-151877600	Weak transcription	Osteobl	bone
17	chr1:151867400-151878600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:151867600-151877200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:151867600-151877600	Weak transcription	NH-A	brain
20	chr1:151868000-151879800	Weak transcription	Liver	Liver
21	chr1:151868000-151880200	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:151868000-151880400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:151868000-151880800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:151871200-151876400	Weak transcription	Psoas Muscle	Psoas
25	chr1:151871400-151877600	Weak transcription	HMEC	breast
26	chr1:151871400-151878800	Weak transcription	Lung	lung
27	chr1:151871400-151878800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:151871400-151879800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:151871400-151880400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:151871600-151876200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr1:151871600-151877000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr1:151871600-151877000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr1:151871600-151877600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:151871600-151877800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:151871800-151876000	Weak transcription	K562	blood
36	chr1:151871800-151878800	Weak transcription	Thymus	Thymus
37	chr1:151872400-151877400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:151872800-151880800	Weak transcription	Right Atrium	heart
39	chr1:151873000-151875400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:151873000-151876000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr1:151873000-151877000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr1:151873000-151880800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:151873600-151875600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:151873600-151877000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:151874400-151877200	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr1:151874400-151878600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:151874600-151875400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:151874800-151875400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:151874800-151877200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:151874800-151877200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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