Variant report

Variant	rs2275780
Chromosome Location	chr1:150241230-150241231
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:316)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:316 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr1:150241212-150241508	GM12878	blood:	n/a	n/a
2	YY1	chr1:150241094-150241696	GM12891	blood:	n/a	n/a
3	YY1	chr1:150240973-150241709	K562	blood:	n/a	n/a
4	POLR2A	chr1:150240381-150241856	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:150241092-150241730	A549	lung:	n/a	n/a
6	BHLHE40	chr1:150241200-150241823	GM12878	blood:	n/a	n/a
7	YY1	chr1:150241056-150241821	SK-N-SH	brain:	n/a	n/a
8	TAF1	chr1:150240941-150241750	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:150241039-150241809	ECC-1	luminal epithelium:	n/a	n/a
10	TCF12	chr1:150240819-150241910	A549	lung:	n/a	chr1:150241047-150241054
11	POLR2A	chr1:150240885-150242031	HepG2	liver:	n/a	n/a
12	E2F6	chr1:150240954-150241607	K562	blood:	n/a	n/a
13	POLR2A	chr1:150240641-150241856	Hela-S3	cervix:	n/a	n/a
14	ELF1	chr1:150241184-150241837	SK-N-SH	brain:	n/a	n/a
15	E2F4	chr1:150241224-150241595	GM12878	blood:	n/a	n/a
16	YY1	chr1:150241043-150241765	A549	lung:	n/a	n/a
17	CREB1	chr1:150241134-150241960	K562	blood:	n/a	n/a
18	POLR2A	chr1:150240521-150241762	GM12891	blood:	n/a	n/a
19	MAX	chr1:150240623-150241980	NB4	blood:	n/a	n/a
20	POLR2A	chr1:150240722-150241870	MCF10A-Er-Src	breast:	n/a	n/a
21	TCF12	chr1:150241181-150241532	A549	lung:	n/a	n/a
22	ELF1	chr1:150241103-150241853	HepG2	liver:	n/a	n/a
23	ZBTB33	chr1:150241196-150241595	A549	lung:	n/a	n/a
24	ELF1	chr1:150241146-150241978	A549	lung:	n/a	n/a
25	POLR2A	chr1:150241124-150241703	HepG2	liver:	n/a	n/a
26	YY1	chr1:150241214-150241645	HepG2	liver:	n/a	n/a
27	MAX	chr1:150240989-150241867	H1-hESC	embryonic stem cell:	n/a	n/a
28	SP4	chr1:150241186-150241845	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr1:150240590-150241861	HL-60	blood:	n/a	n/a
30	TEAD4	chr1:150241103-150241703	K562	blood:	n/a	n/a
31	MAX	chr1:150240562-150241825	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr1:150241200-150241435	HepG2	liver:	n/a	n/a
33	GABPA	chr1:150241224-150241719	HepG2	liver:	n/a	n/a
34	SRF	chr1:150240669-150241965	MCF-7	breast:	n/a	chr1:150241080-150241090
35	SIN3AK20	chr1:150241064-150241730	SK-N-SH	brain:	n/a	n/a
36	ELF1	chr1:150241104-150241950	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr1:150240573-150241828	GM12891	blood:	n/a	n/a
38	ETS1	chr1:150241118-150241782	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:150240687-150241722	GM12878	blood:	n/a	n/a
40	ZBTB33	chr1:150241160-150241716	HCT-116	colon:	n/a	n/a
41	MXI1	chr1:150241103-150241764	HepG2	liver:	n/a	n/a
42	TAF1	chr1:150240761-150241995	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr1:150240659-150241813	K562	blood:	n/a	n/a
44	ELF1	chr1:150240655-150241760	GM12878	blood:	n/a	n/a
45	NR2F2	chr1:150240598-150242099	K562	blood:	n/a	n/a
46	TAF1	chr1:150240735-150241843	ECC-1	luminal epithelium:	n/a	n/a
47	SIX5	chr1:150241218-150241799	GM12878	blood:	n/a	n/a
48	ZBTB7A	chr1:150240962-150241664	ECC-1	luminal epithelium:	n/a	n/a
49	SIN3AK20	chr1:150240992-150241718	PANC-1	pancreas:	n/a	n/a
50	POLR2A	chr1:150241014-150241800	Hela-S3	cervix:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:149857136..149859166-chr1:150238966..150241520,2	K562	blood:
2	chr1:150207289..150210046-chr1:150241185..150243177,3	MCF-7	breast:
3	chr1:150237764..150241503-chr1:150313486..150318525,4	MCF-7	breast:
4	chr1:150240799..150242755-chr1:150334348..150335863,2	MCF-7	breast:
5	chr1:150204090..150209498-chr1:150239337..150243073,9	K562	blood:
6	chr1:150240546..150242221-chr1:150264940..150266566,2	K562	blood:
7	chr1:150206345..150209742-chr1:150239312..150243074,6	K562	blood:
8	chr1:150240117..150242604-chr1:150335915..150338709,4	MCF-7	breast:
9	chr1:150240934..150241485-chr14:24682246..24682842,2	Hela-S3	cervix:
10	chr1:150227702..150230865-chr1:150236687..150241657,6	K562	blood:
11	chr1:150240223..150242953-chr1:150263372..150266971,3	K562	blood:
12	chr1:150121990..150123693-chr1:150240466..150243151,2	K562	blood:
13	chr1:149855851..149859969-chr1:150239672..150242215,4	MCF-7	breast:
14	chr1:150241010..150241781-chr22:47158212..47158810,2	HCT-116	colon:
15	chr1:150238576..150241529-chr1:150952972..150954986,2	MCF-7	breast:
16	chr1:150206579..150210456-chr1:150238390..150242863,9	MCF-7	breast:

No data

Variant related genes	Relation type
C1orf54	TF binding region
APH1A	TF binding region
ENSG00000118298	Chromatin interaction
ENSG00000143412	Chromatin interaction
ENSG00000260708	Chromatin interaction
ENSG00000143401	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000271845	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000222222	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000054611	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000117360	Chromatin interaction
ENSG00000187145	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10494266	0.89[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12027008	1.00[ASW][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes]
rs12129776	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs956796	1.00[ASW][hapmap]

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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2275780	MRPS21	cis	parietal	SCAN
rs2275780	MRPS21	cis	cerebellum	SCAN
rs2275780	CTSS	cis	cerebellum	SCAN
rs2275780	TMOD4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150239800-150242600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:150240000-150241800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:150240000-150242000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:150240000-150242000	Active TSS	Psoas Muscle	Psoas
5	chr1:150240000-150242400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:150240000-150242400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:150240000-150242400	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr1:150240000-150242600	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:150240200-150241400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:150240200-150241400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:150240200-150242000	Active TSS	Muscle Satellite Cultured Cells	--
12	chr1:150240200-150242200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:150240200-150242200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:150240200-150242200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:150240200-150242400	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr1:150240400-150241400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:150240400-150241600	Active TSS	K562	blood
18	chr1:150240400-150241600	Active TSS	NHLF	lung
19	chr1:150240400-150241800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:150240400-150241800	Active TSS	Lung	lung
21	chr1:150240400-150241800	Active TSS	Ovary	ovary
22	chr1:150240400-150241800	Active TSS	Small Intestine	intestine
23	chr1:150240400-150241800	Active TSS	HepG2	liver
24	chr1:150240400-150242000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:150240400-150242000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:150240400-150242000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:150240400-150242000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:150240400-150242000	Active TSS	Left Ventricle	heart
29	chr1:150240400-150242000	Active TSS	GM12878-XiMat	blood
30	chr1:150240400-150242000	Active TSS	NHDF-Ad	bronchial
31	chr1:150240400-150242200	Active TSS	A549	lung
32	chr1:150240400-150242200	Active TSS	HSMM	muscle
33	chr1:150240600-150241600	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr1:150240600-150241600	Active TSS	NH-A	brain
35	chr1:150240600-150241800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:150240600-150241800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:150240600-150241800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:150240600-150241800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:150240600-150241800	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr1:150240600-150241800	Active TSS	Aorta	Aorta
41	chr1:150240600-150241800	Active TSS	Brain Cingulate Gyrus	brain
42	chr1:150240600-150241800	Active TSS	Esophagus	oesophagus
43	chr1:150240600-150241800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr1:150240600-150241800	Active TSS	Fetal Heart	heart
45	chr1:150240600-150241800	Active TSS	Fetal Intestine Small	intestine
46	chr1:150240600-150241800	Active TSS	Gastric	stomach
47	chr1:150240600-150241800	Active TSS	Pancreas	Pancrea
48	chr1:150240600-150241800	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr1:150240600-150241800	Active TSS	Stomach Mucosa	stomach
50	chr1:150240600-150241800	Active TSS	Spleen	Spleen

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