Variant report

Variant	rs12067594
Chromosome Location	chr1:151865780-151865781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151864758..151867569-chr1:151867706..151869212,2	K562	blood:
2	chr1:151858712..151862714-chr1:151863688..151869439,8	K562	blood:
3	chr1:151864865..151867501-chr1:151960955..151964248,3	MCF-7	breast:
4	chr1:151861522..151872673-chr1:151876647..151885029,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1038747	0.81[AMR][1000 genomes]
rs1060870	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10788817	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10788818	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10788820	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10888445	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204914	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11204915	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12116923	0.86[AMR][1000 genomes]
rs12562586	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13320	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1387833	0.87[AMR][1000 genomes]
rs1490189	0.87[AMR][1000 genomes]
rs1907040	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2130525	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2279501	0.85[AMR][1000 genomes]
rs2279502	0.86[AMR][1000 genomes]
rs2338201	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2338209	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2932565	0.88[AMR][1000 genomes]
rs2932576	0.87[AMR][1000 genomes]
rs2932577	0.87[AMR][1000 genomes]
rs2932579	0.87[AMR][1000 genomes]
rs2932583	0.84[AMR][1000 genomes]
rs2999506	0.87[AMR][1000 genomes]
rs2999541	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2999542	0.87[AMR][1000 genomes]
rs2999544	0.88[AMR][1000 genomes]
rs2999545	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2999546	0.87[AMR][1000 genomes]
rs3007670	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3007685	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3007691	0.84[AMR][1000 genomes]
rs3007711	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4845409	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4845713	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6685187	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698740	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7523082	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7541453	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7542137	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9435963	0.88[AMR][1000 genomes]
rs9435964	0.88[AMR][1000 genomes]
rs9943281	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12067594	THEM4	cis	Nerve Tibial	GTEx
rs12067594	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs12067594	THEM4	cis	Esophagus Muscularis	GTEx
rs12067594	S100A10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151831000-151881400	Weak transcription	Ovary	ovary
2	chr1:151841200-151880800	Weak transcription	NHLF	lung
3	chr1:151844400-151866400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:151844400-151881200	Weak transcription	Aorta	Aorta
5	chr1:151844800-151870800	Weak transcription	Gastric	stomach
6	chr1:151844800-151871200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:151844800-151877600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:151845400-151871200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:151846400-151870400	Weak transcription	Right Ventricle	heart
10	chr1:151846400-151871600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:151847000-151869600	Weak transcription	Small Intestine	intestine
12	chr1:151847000-151871000	Weak transcription	Spleen	Spleen
13	chr1:151847400-151870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:151851000-151871200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:151854000-151880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:151857000-151873000	Weak transcription	GM12878-XiMat	blood
17	chr1:151857600-151873400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:151857600-151874200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:151857800-151866600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:151857800-151867800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:151857800-151868400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:151858000-151866400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:151858000-151867800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:151858000-151868000	Strong transcription	Fetal Intestine Large	intestine
25	chr1:151858000-151868000	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:151858000-151868400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:151859400-151870800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:151859600-151868400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:151859600-151869200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr1:151859600-151870600	Weak transcription	HepG2	liver
31	chr1:151860000-151868600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:151860600-151865800	Weak transcription	NHDF-Ad	bronchial
33	chr1:151860600-151871800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:151860600-151877600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:151860800-151879800	Weak transcription	Brain Angular Gyrus	brain
36	chr1:151861400-151866000	Weak transcription	HMEC	breast
37	chr1:151861600-151879800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:151861800-151867400	Strong transcription	Hela-S3	cervix
39	chr1:151862400-151870400	Weak transcription	Psoas Muscle	Psoas
40	chr1:151862400-151880400	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:151863000-151867400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr1:151863000-151868400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:151863000-151869600	Weak transcription	Colonic Mucosa	Colon
44	chr1:151863200-151870600	Weak transcription	Esophagus	oesophagus
45	chr1:151863600-151866000	Weak transcription	HSMM	muscle
46	chr1:151863600-151866200	Strong transcription	Fetal Kidney	kidney
47	chr1:151863600-151868000	Strong transcription	Brain Hippocampus Middle	brain
48	chr1:151863600-151868200	Strong transcription	Left Ventricle	heart
49	chr1:151863800-151868000	Strong transcription	Fetal Muscle Leg	muscle
50	chr1:151863800-151869000	Weak transcription	Placenta	Placenta

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