Variant report

Variant	rs7660054
Chromosome Location	chr4:56268507-56268508
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	POLR2A	chr4:56268360-56274870	K562	blood:	n/a	n/a
2	POLR2A	chr4:56268244-56268530	K562	blood:	n/a	n/a
3	POLR2A	chr4:56268475-56270582	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56261651..56266514-chr4:56267808..56271520,10	MCF-7	breast:
2	chr4:56211148..56230966-chr4:56256626..56269458,54	MCF-7	breast:
3	chr4:56211281..56215987-chr4:56257992..56268538,18	K562	blood:
4	chr4:56210761..56214527-chr4:56265668..56271169,8	K562	blood:

Variant related genes	Relation type
TMEM165	TF binding region
ENSG00000249700	Chromatin interaction
ENSG00000128039	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000251111	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10002541	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10005989	1.00[CEU][hapmap]
rs10016506	0.86[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap]
rs10026692	0.96[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap]
rs1011095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11133376	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11133379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11133383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs11133399	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs1128141	0.88[ASN][1000 genomes]
rs11726609	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs11733864	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11735267	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11931061	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs11939815	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[EUR][1000 genomes]
rs11947476	0.81[EUR][1000 genomes]
rs11947623	0.81[EUR][1000 genomes]
rs13102385	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs13121235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13128582	0.82[EUR][1000 genomes]
rs13138697	0.81[EUR][1000 genomes]
rs13152650	0.81[EUR][1000 genomes]
rs1522106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs1522110	0.80[EUR][1000 genomes]
rs1522111	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1873092	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.93[TSI][hapmap]
rs1965467	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1980273	0.80[EUR][1000 genomes]
rs2140077	0.81[EUR][1000 genomes]
rs2177127	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs2177129	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2412646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2412647	0.83[EUR][1000 genomes]
rs2412663	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs28665088	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28726308	0.82[EUR][1000 genomes]
rs2899037	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs35767091	0.81[EUR][1000 genomes]
rs3736544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs3736545	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3805147	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3805154	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs3805157	0.81[EUR][1000 genomes]
rs3817444	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.95[TSI][hapmap]
rs4580704	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs473005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs480479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4864998	0.81[EUR][1000 genomes]
rs4865010	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs4865018	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs501679	0.92[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs564762	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs576779	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62303714	0.82[EUR][1000 genomes]
rs6554286	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs6811520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs6812042	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs6815516	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6817267	0.81[EUR][1000 genomes]
rs6819660	0.80[EUR][1000 genomes]
rs6824955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs6829182	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap]
rs6832769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs6834676	0.83[EUR][1000 genomes]
rs6837710	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6850524	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6851838	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6853192	0.96[CEU][hapmap]
rs726967	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7667849	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs7673908	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs7677526	0.81[EUR][1000 genomes]
rs7684810	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs819271	0.92[CEU][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs9312662	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs9993675	0.92[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs9997288	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
5	esv3513387	chr4:56265445-56270643	Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3513386	chr4:56265495-56269293	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3513388	chr4:56265495-56269293	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv594204	chr4:56266973-56268507	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56264200-56269800	Weak transcription	Spleen	Spleen
2	chr4:56264200-56270200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:56264200-56273000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:56264600-56270000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr4:56264800-56269800	Weak transcription	Fetal Kidney	kidney
6	chr4:56264800-56282200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:56264800-56292200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:56265000-56273200	Weak transcription	Gastric	stomach
9	chr4:56265400-56273400	Weak transcription	Aorta	Aorta
10	chr4:56265600-56269200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:56265600-56269200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:56265600-56269200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:56265600-56269200	Weak transcription	HSMMtube	muscle
14	chr4:56265600-56269800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:56265600-56269800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:56265600-56269800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:56265600-56269800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:56265600-56269800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:56265600-56270200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:56265600-56270200	Weak transcription	Lung	lung
21	chr4:56265600-56270200	Weak transcription	Thymus	Thymus
22	chr4:56265600-56271400	Weak transcription	Psoas Muscle	Psoas
23	chr4:56265600-56271800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:56265600-56272000	Weak transcription	Esophagus	oesophagus
25	chr4:56265600-56272200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:56265600-56273200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:56265600-56273800	Weak transcription	Stomach Mucosa	stomach
28	chr4:56265600-56275600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:56265600-56281600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:56265600-56283800	Weak transcription	Fetal Brain Male	brain
31	chr4:56265600-56286000	Weak transcription	Colonic Mucosa	Colon
32	chr4:56265600-56289800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr4:56265800-56269400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:56265800-56271400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:56265800-56271600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:56265800-56271600	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:56265800-56274400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:56265800-56275200	Weak transcription	Fetal Heart	heart
40	chr4:56265800-56281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:56266000-56269200	Weak transcription	Fetal Intestine Large	intestine
42	chr4:56266000-56269400	Weak transcription	HMEC	breast
43	chr4:56266000-56269800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr4:56266000-56269800	Weak transcription	NHLF	lung
45	chr4:56266000-56270000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:56266000-56270200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:56266000-56270600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:56266000-56271800	Weak transcription	Fetal Brain Female	brain
49	chr4:56266000-56272000	Weak transcription	Brain Germinal Matrix	brain
50	chr4:56266000-56283200	Weak transcription	Rectal Smooth Muscle	rectum

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