Variant report

Variant	rs677277
Chromosome Location	chr1:120202298-120202299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:120202130-120202608	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr1:120202262-120202648	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAZ	chr1:120202110-120202680	IMR90	lung:	n/a	n/a
4	TEAD4	chr1:120202143-120202573	H1-hESC	embryonic stem cell:	n/a	n/a
5	HDAC2	chr1:120202190-120202519	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF12	chr1:120202295-120202486	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr1:120201951-120202551	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr1:120202191-120202519	H1-hESC	embryonic stem cell:	n/a	n/a
9	CEBPB	chr1:120202145-120202498	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr1:120202219-120202637	H1-hESC	embryonic stem cell:	n/a	n/a
11	CHD2	chr1:120202229-120202770	H1-hESC	embryonic stem cell:	n/a	n/a
12	CEBPB	chr1:120202198-120202461	IMR90	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:120201333..120204049-chr1:120254351..120256217,2	MCF-7	breast:
2	chr1:120188763..120191080-chr1:120201790..120203315,2	K562	blood:
3	chr1:120188687..120197065-chr1:120197482..120205927,19	MCF-7	breast:
4	chr1:120187998..120191080-chr1:120201790..120203947,3	K562	blood:

No data

Variant related genes	Relation type
PHGDH	TF binding region
ENSG00000092621	Chromatin interaction
ENSG00000143067	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1163251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2764886	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs477992	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs478093	0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs478450	0.82[EUR][1000 genomes]
rs483180	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs483360	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487081	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs487884	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs493427	0.86[CEU][hapmap]
rs496195	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs496198	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs511059	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs514491	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs517533	0.86[EUR][1000 genomes]
rs539708	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs539799	0.82[CEU][hapmap]
rs541503	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs561931	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs592762	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs594400	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs595283	0.82[EUR][1000 genomes]
rs597308	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs598685	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs606312	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs611365	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs612430	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs627707	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs629735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs639216	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs639761	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs640195	0.95[EUR][1000 genomes]
rs658442	0.86[EUR][1000 genomes]
rs660073	0.85[EUR][1000 genomes]
rs662243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs662602	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs666930	0.85[CHD][hapmap]
rs839600	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs839605	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs839607	0.80[EUR][1000 genomes]
rs839608	0.93[EUR][1000 genomes]
rs866321	0.94[EUR][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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2757749	chr1:120016696-120214577	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv2758964	chr1:120016696-120214577	Enhancers ZNF genes & repeats Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120193600-120202400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:120198200-120202400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:120199400-120204600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:120201600-120203800	Enhancers	Fetal Lung	lung
5	chr1:120202000-120202600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:120202000-120203400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:120202000-120203600	Enhancers	Fetal Kidney	kidney
8	chr1:120202000-120203800	Enhancers	Fetal Stomach	stomach
9	chr1:120202000-120206000	Enhancers	Fetal Intestine Small	intestine
10	chr1:120202200-120202400	Enhancers	H9 Cell Line	embryonic stem cell
11	chr1:120202200-120202400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:120202200-120202600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:120202200-120202600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:120202200-120202600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:120202200-120202600	Enhancers	Fetal Muscle Trunk	muscle
16	chr1:120202200-120202600	Enhancers	Lung	lung
17	chr1:120202200-120202600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
18	chr1:120202200-120202800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr1:120202200-120202800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr1:120202200-120202800	Enhancers	Gastric	stomach
21	chr1:120202200-120202800	Enhancers	Ovary	ovary
22	chr1:120202200-120202800	Enhancers	Pancreas	Pancrea
23	chr1:120202200-120203000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:120202200-120203000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr1:120202200-120203000	Enhancers	Liver	Liver
26	chr1:120202200-120203000	Enhancers	Fetal Heart	heart
27	chr1:120202200-120203400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:120202200-120203400	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr1:120202200-120203400	Enhancers	Fetal Muscle Leg	muscle
30	chr1:120202200-120203400	Enhancers	Placenta	Placenta
31	chr1:120202200-120203400	Enhancers	Small Intestine	intestine
32	chr1:120202200-120203600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr1:120202200-120204200	Enhancers	GM12878-XiMat	blood
34	chr1:120202200-120205000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:120202200-120205400	Enhancers	Duodenum Mucosa	Duodenum
36	chr1:120202200-120206000	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr1:120202200-120206200	Enhancers	Fetal Intestine Large	intestine

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