Variant report

Variant	rs880358
Chromosome Location	chr4:56276478-56276479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:56276262-56276503	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:56266974..56269917-chr4:56274406..56277195,2	MCF-7	breast:
2	chr4:56275809..56278262-chr4:56283958..56286779,2	K562	blood:
3	chr4:56212034..56214727-chr4:56273890..56277792,4	MCF-7	breast:
4	chr4:56275357..56276969-chr4:56278141..56280146,2	K562	blood:
5	chr4:56275450..56278290-chr4:56412391..56414503,2	K562	blood:
6	chr4:56211324..56213872-chr4:56274081..56277036,2	K562	blood:

No data

Variant related genes	Relation type
TMEM165	TF binding region
ENSG00000239040	TF binding region
ENSG00000134851	Chromatin interaction
ENSG00000128039	Chromatin interaction
ENSG00000134852	Chromatin interaction
ENSG00000272969	Chromatin interaction
ENSG00000239040	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10010762	0.84[ASN][1000 genomes]
rs10012559	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10021233	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs10024928	0.84[ASN][1000 genomes]
rs1021306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1021307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10462028	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.89[ASN][1000 genomes]
rs1048004	0.85[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11732481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs11732723	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs11932595	1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs11943456	1.00[JPT][hapmap]
rs13133077	0.86[CEU][hapmap]
rs17721215	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17721497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17722870	0.81[EUR][1000 genomes]
rs17722979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap]
rs17776975	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1979604	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1979605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2101476	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs2130040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2412664	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]
rs2538	0.81[JPT][hapmap]
rs3087606	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3792603	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs41324951	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4336288	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4455482	0.84[ASN][1000 genomes]
rs475465	0.84[ASN][1000 genomes]
rs476184	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs482114	0.89[ASN][1000 genomes]
rs483978	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.89[ASN][1000 genomes]
rs4865012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs496055	0.84[ASN][1000 genomes]
rs499110	0.84[ASN][1000 genomes]
rs525271	0.84[ASN][1000 genomes]
rs550144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs552792	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs552950	0.84[ASN][1000 genomes]
rs556072	0.84[ASN][1000 genomes]
rs56056791	0.81[EUR][1000 genomes]
rs56139168	1.00[ASN][1000 genomes]
rs572428	0.89[ASN][1000 genomes]
rs572553	0.89[ASN][1000 genomes]
rs576732	0.82[CHD][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs58176292	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58506276	0.84[ASN][1000 genomes]
rs59648459	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60097207	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62303681	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62303685	0.93[ASN][1000 genomes]
rs62303686	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62303690	0.86[ASN][1000 genomes]
rs62303691	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62303692	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62303708	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62303709	0.86[ASN][1000 genomes]
rs62303711	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62303712	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62303713	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62303718	0.81[EUR][1000 genomes]
rs62303722	0.82[AMR][1000 genomes]
rs62303728	0.84[AMR][1000 genomes]
rs62305200	0.84[ASN][1000 genomes]
rs62305201	0.86[ASN][1000 genomes]
rs62305202	0.86[ASN][1000 genomes]
rs62305206	0.86[ASN][1000 genomes]
rs62306207	0.84[ASN][1000 genomes]
rs6554290	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.94[TSI][hapmap]
rs6554291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs67963898	0.81[EUR][1000 genomes]
rs6802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6830728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6842960	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6851971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6853506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6858749	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs693367	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[ASN][1000 genomes]
rs73236140	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73236142	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7659095	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7660668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7665846	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7676245	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7698022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs819203	0.86[ASN][1000 genomes]
rs819266	0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs819268	0.81[JPT][hapmap]
rs819269	0.81[TSI][hapmap]
rs819270	0.81[JPT][hapmap]
rs861029	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs972446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs9993599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]

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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs880358	TMEM165	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56264800-56282200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:56264800-56292200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:56265600-56281600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:56265600-56283800	Weak transcription	Fetal Brain Male	brain
5	chr4:56265600-56286000	Weak transcription	Colonic Mucosa	Colon
6	chr4:56265600-56289800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:56265800-56281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr4:56266000-56283200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:56267400-56280800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:56267400-56282800	Weak transcription	Small Intestine	intestine
12	chr4:56267400-56283200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr4:56267600-56280800	Weak transcription	A549	lung
14	chr4:56268800-56326000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:56269000-56311400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr4:56270000-56281000	Weak transcription	Fetal Kidney	kidney
17	chr4:56270200-56281000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:56270200-56281600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:56270200-56282800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr4:56270400-56277400	Weak transcription	Hela-S3	cervix
21	chr4:56270400-56286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:56271800-56277800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:56272400-56278000	Weak transcription	Esophagus	oesophagus
24	chr4:56272400-56281000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:56272600-56277800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:56272600-56282800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:56273200-56279600	Weak transcription	Fetal Brain Female	brain
28	chr4:56273400-56277600	Weak transcription	HMEC	breast
29	chr4:56273400-56277800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:56273400-56283200	Weak transcription	Brain Germinal Matrix	brain
31	chr4:56273600-56277600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr4:56273600-56277800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:56273600-56277800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:56273600-56277800	Weak transcription	Fetal Intestine Small	intestine
35	chr4:56273600-56277800	Weak transcription	Fetal Stomach	stomach
36	chr4:56273600-56277800	Weak transcription	Lung	lung
37	chr4:56273600-56282200	Weak transcription	Pancreas	Pancrea
38	chr4:56273800-56276800	Weak transcription	Placenta	Placenta
39	chr4:56273800-56281600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr4:56273800-56283200	Weak transcription	Psoas Muscle	Psoas
41	chr4:56274200-56277400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:56274200-56277800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr4:56274200-56277800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:56274200-56277800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:56274200-56277800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr4:56274200-56277800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr4:56274200-56277800	Weak transcription	Thymus	Thymus
48	chr4:56274200-56280200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr4:56274200-56280200	Weak transcription	Fetal Intestine Large	intestine
50	chr4:56274200-56280800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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