Variant report

Variant	rs2275778
Chromosome Location	chr1:150239478-150239479
allele	G/T
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:9)
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	POLR2A	chr1:150239477-150239585	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:149857136..149859166-chr1:150238966..150241520,2	K562	blood:
2	chr1:150207728..150209520-chr1:150239251..150240974,2	MCF-7	breast:
3	chr1:150237764..150241503-chr1:150313486..150318525,4	MCF-7	breast:
4	chr1:150204090..150209498-chr1:150239337..150243073,9	K562	blood:
5	chr1:150206345..150209742-chr1:150239312..150243074,6	K562	blood:
6	chr1:150227702..150230865-chr1:150236687..150241657,6	K562	blood:
7	chr1:150238105..150240818-chr1:150533099..150535051,3	MCF-7	breast:
8	chr1:150238576..150241529-chr1:150952972..150954986,2	MCF-7	breast:
9	chr1:150206579..150210456-chr1:150238390..150242863,9	MCF-7	breast:

No data

Variant related genes	Relation type
C1orf54	TF binding region
ENSG00000118298	Chromatin interaction
ENSG00000117360	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000222222	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000143412	Chromatin interaction
ENSG00000271845	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs16830437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16835699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16835708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16835782	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16835791	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16835911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16836130	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16836139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16836442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16836576	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs16836594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16836601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16836786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16836940	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs16836943	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1694386	0.84[JPT][hapmap]
rs2015966	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2275779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3737319	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3738322	0.87[ASN][1000 genomes]
rs3850843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4926420	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4926421	1.00[JPT][hapmap]
rs522068	0.83[ASN][1000 genomes]
rs56882505	0.81[ASN][1000 genomes]
rs56909494	0.81[ASN][1000 genomes]
rs57163995	0.85[ASN][1000 genomes]
rs57361164	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58373639	0.82[AMR][1000 genomes]
rs58516261	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59367061	0.81[ASN][1000 genomes]
rs59639798	0.81[ASN][1000 genomes]
rs60456922	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60459288	0.81[ASN][1000 genomes]
rs60531845	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60730811	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60758881	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6679726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6700009	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6700607	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs71622690	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73011380	0.98[ASN][1000 genomes]
rs73011384	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73011400	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73013119	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73013129	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73015063	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73015078	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73015081	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73015095	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73015096	0.85[ASN][1000 genomes]
rs73017006	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73017073	0.81[ASN][1000 genomes]
rs73017086	0.81[ASN][1000 genomes]
rs7543314	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
3	nsv872415	chr1:150210538-150248046	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1009508	chr1:150211112-150270830	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv535154	chr1:150214907-150265508	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1011223	chr1:150229205-150279380	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150232600-150240400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:150233000-150239800	Strong transcription	H1 Cell Line	embryonic stem cell
3	chr1:150233200-150239600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:150233200-150239800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:150233200-150240200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:150233600-150239600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:150233600-150239800	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr1:150233600-150239800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:150233600-150239800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:150233800-150239800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:150234000-150239800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:150234800-150239800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:150235400-150239800	Strong transcription	Fetal Stomach	stomach
14	chr1:150235600-150239600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:150235600-150239600	Strong transcription	Brain Cingulate Gyrus	brain
16	chr1:150235800-150239600	Strong transcription	Fetal Muscle Leg	muscle
17	chr1:150235800-150239800	Weak transcription	Small Intestine	intestine
18	chr1:150236000-150239600	Strong transcription	Right Ventricle	heart
19	chr1:150236000-150239800	Strong transcription	Primary T cells from cord blood	blood
20	chr1:150236200-150239600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:150236200-150239800	Weak transcription	Stomach Mucosa	stomach
22	chr1:150236600-150239600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:150236600-150239600	Strong transcription	Adipose Nuclei	Adipose
24	chr1:150236600-150239600	Strong transcription	Aorta	Aorta
25	chr1:150236600-150239800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:150236800-150239600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:150236800-150239600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:150236800-150239600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:150236800-150239600	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr1:150236800-150239600	Strong transcription	Liver	Liver
31	chr1:150236800-150239600	Strong transcription	Placenta	Placenta
32	chr1:150236800-150239800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:150236800-150239800	Strong transcription	Fetal Intestine Large	intestine
34	chr1:150236800-150239800	Strong transcription	Thymus	Thymus
35	chr1:150236800-150240000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:150237000-150239600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:150237000-150239600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr1:150237000-150239600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:150237000-150239600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:150237000-150239600	Strong transcription	Brain Substantia Nigra	brain
41	chr1:150237000-150239600	Strong transcription	HSMM	muscle
42	chr1:150237000-150239600	Strong transcription	HUVEC	blood vessel
43	chr1:150237000-150239600	Strong transcription	K562	blood
44	chr1:150237000-150239600	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:150237000-150239600	Strong transcription	NHLF	lung
46	chr1:150237000-150239600	Strong transcription	Osteobl	bone
47	chr1:150237000-150239800	Strong transcription	Primary hematopoietic stem cells	blood
48	chr1:150237000-150239800	Strong transcription	Fetal Brain Female	brain
49	chr1:150237000-150239800	Strong transcription	Fetal Lung	lung
50	chr1:150237000-150239800	Strong transcription	Ovary	ovary

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