Variant report

Variant	rs2039230
Chromosome Location	chr1:176174791-176174792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr1:176174357-176175093	K562	blood:	n/a	chr1:176174707-176174720 chr1:176174708-176174722 chr1:176175055-176175065
2	FOS	chr1:176174698-176175050	MCF10A-Er-Src	breast:	n/a	n/a
3	E2F4	chr1:176174648-176175398	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:176174664-176175064	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr1:176174619-176175076	MCF10A-Er-Src	breast:	n/a	n/a
6	MXI1	chr1:176174331-176177577	SK-N-SH	brain:	n/a	n/a
7	UBTF	chr1:176174742-176177096	K562	blood:	n/a	n/a
8	FOS	chr1:176174363-176174914	HUVEC	blood vessel:	n/a	n/a
9	MXI1	chr1:176174606-176177275	IMR90	lung:	n/a	n/a
10	IRF1	chr1:176174148-176174977	K562	blood:	n/a	chr1:176174707-176174720 chr1:176174708-176174722
11	STAT3	chr1:176174781-176174982	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr1:176174599-176175049	MCF10A-Er-Src	breast:	n/a	n/a
13	HCFC1	chr1:176174420-176177567	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:176174704-176177271	PBDE	blood:	n/a	n/a
15	CUX1	chr1:176174130-176175104	K562	blood:	n/a	chr1:176174549-176174558
16	POLR2A	chr1:176174335-176179842	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:176159070..176161362-chr1:176173225..176174837,2	K562	blood:
2	chr1:176173011..176175241-chr1:176190207..176192824,3	K562	blood:
3	chr1:176153551..176156175-chr1:176174165..176176640,2	K562	blood:
4	chr1:176152065..176154740-chr1:176172886..176175167,2	MCF-7	breast:
5	chr1:176174633..176176230-chr7:139024705..139027215,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236021	TF binding region
ENSG00000146963	Chromatin interaction
ENSG00000143207	Chromatin interaction
ENSG00000269955	Chromatin interaction
ENSG00000164898	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10753117	0.91[JPT][hapmap]
rs10798442	0.91[JPT][hapmap]
rs10798445	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10798446	0.86[JPT][hapmap]
rs10913135	0.85[JPT][hapmap]
rs10913137	0.86[JPT][hapmap]
rs10913143	0.86[JPT][hapmap]
rs10913144	0.86[JPT][hapmap]
rs10913147	0.86[JPT][hapmap]
rs10913152	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11810706	0.95[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs12029090	0.89[JPT][hapmap]
rs12033847	0.91[JPT][hapmap]
rs12049077	0.86[JPT][hapmap]
rs12117377	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12138008	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs12404596	0.91[JPT][hapmap]
rs12729524	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12758275	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17354120	0.86[JPT][hapmap]
rs1858537	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs191606	0.81[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes]
rs1974142	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2102479	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2175177	0.90[JPT][hapmap]
rs2175178	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2455730	0.86[AMR][1000 genomes]
rs2455732	0.86[AMR][1000 genomes]
rs2455749	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2455762	0.82[AMR][1000 genomes]
rs2457418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2481628	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2481630	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2481631	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2481633	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2481655	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2481662	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2487144	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2502823	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs2502831	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2502845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504493	0.86[JPT][hapmap]
rs2504501	0.86[AMR][1000 genomes]
rs35907544	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3962371	0.86[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4298694	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs482228	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs501142	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513354	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs520661	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs534088	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs542742	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs596859	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617078	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs659279	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665385	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6678628	0.86[JPT][hapmap]
rs6678812	0.86[JPT][hapmap]
rs668154	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6687280	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6697860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6700932	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs670143	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679728	0.86[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs704829	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs704834	0.86[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71645275	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7517503	0.86[JPT][hapmap]
rs7535769	0.86[CEU][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7549160	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs791743	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791746	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791747	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791750	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791751	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791752	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791753	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs813180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425447	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs944365	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2039230	EME2	trans	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
2	chr1:176166000-176175400	Weak transcription	Spleen	Spleen
3	chr1:176171600-176175200	Weak transcription	Gastric	stomach
4	chr1:176171600-176175400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:176171800-176175200	Weak transcription	Lung	lung
6	chr1:176172400-176174800	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr1:176173000-176174800	Enhancers	Brain Cingulate Gyrus	brain
8	chr1:176173000-176175200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr1:176173000-176175200	Flanking Active TSS	Dnd41	blood
10	chr1:176173400-176174800	Weak transcription	Fetal Stomach	stomach
11	chr1:176173400-176175400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr1:176173600-176174800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:176173600-176174800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr1:176173600-176175000	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr1:176173600-176175800	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr1:176173600-176175800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:176173600-176176000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr1:176173800-176174800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:176173800-176174800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr1:176173800-176174800	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr1:176173800-176175000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:176173800-176175000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr1:176173800-176175400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:176173800-176175800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:176173800-176177600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:176173800-176177600	Active TSS	HSMM	muscle
27	chr1:176174000-176174800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr1:176174000-176175000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:176174000-176175000	Flanking Active TSS	Fetal Brain Female	brain
30	chr1:176174000-176175000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr1:176174000-176175000	Weak transcription	Small Intestine	intestine
32	chr1:176174000-176175000	Flanking Active TSS	HMEC	breast
33	chr1:176174000-176175200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr1:176174000-176175400	Flanking Active TSS	Hela-S3	cervix
35	chr1:176174000-176175600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:176174000-176175800	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr1:176174000-176177200	Active TSS	Fetal Intestine Small	intestine
38	chr1:176174000-176177400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr1:176174000-176177400	Active TSS	Right Ventricle	heart
40	chr1:176174000-176177600	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:176174000-176177600	Active TSS	HSMMtube	muscle
42	chr1:176174200-176174800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:176174200-176174800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr1:176174200-176175000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr1:176174200-176175000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:176174200-176175000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr1:176174200-176175000	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr1:176174200-176175000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr1:176174200-176175000	Flanking Active TSS	Fetal Brain Male	brain
50	chr1:176174200-176175000	Weak transcription	Fetal Muscle Trunk	muscle

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