Variant report

Variant	rs202053
Chromosome Location	chr6:13273643-13273644
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:109)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:109 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr6:13273499-13275049	GM18951	blood:	n/a	n/a
2	MAX	chr6:13273433-13273821	K562	blood:	n/a	n/a
3	POLR2A	chr6:13273339-13273728	GM12891	blood:	n/a	n/a
4	ARID3A	chr6:13272972-13275162	K562	blood:	n/a	n/a
5	POLR2A	chr6:13272680-13275076	K562	blood:	n/a	n/a
6	MTA3	chr6:13272472-13275024	GM12878	blood:	n/a	n/a
7	BHLHE40	chr6:13272403-13274607	K562	blood:	n/a	chr6:13272899-13272908 chr6:13272899-13272908 chr6:13272900-13272909 chr6:13272874-13272890 chr6:13272849-13272865 chr6:13272893-13272914
8	ZMIZ1	chr6:13272751-13273735	K562	blood:	n/a	n/a
9	ZNF384	chr6:13273469-13273935	K562	blood:	n/a	n/a
10	REST	chr6:13273423-13273763	K562	blood:	n/a	n/a
11	BACH1	chr6:13273445-13273855	K562	blood:	n/a	n/a
12	MAFF	chr6:13273043-13273937	K562	blood:	n/a	n/a
13	NFATC1	chr6:13273370-13275112	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:13273626-13274997	GM19193	blood:	n/a	n/a
15	TBP	chr6:13272787-13273735	K562	blood:	n/a	n/a
16	MYC	chr6:13272686-13275149	K562	blood:	n/a	chr6:13272870-13272880
17	RCOR1	chr6:13273358-13273806	K562	blood:	n/a	n/a
18	HEY1	chr6:13273454-13273783	K562	blood:	n/a	n/a
19	MAX	chr6:13272344-13273697	NB4	blood:	n/a	chr6:13272870-13272880
20	JUN	chr6:13272018-13276804	K562	blood:	n/a	chr6:13276647-13276657
21	POLR2A	chr6:13272688-13273666	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:13273189-13273763	GM12891	blood:	n/a	n/a
23	YY1	chr6:13273406-13273772	K562	blood:	n/a	n/a
24	RCOR1	chr6:13273403-13274938	K562	blood:	n/a	n/a
25	IRF1	chr6:13273314-13273961	K562	blood:	n/a	n/a
26	RELA	chr6:13272294-13275127	GM12891	blood:	n/a	n/a
27	POLR2A	chr6:13271984-13273855	K562	blood:	n/a	n/a
28	E2F6	chr6:13273573-13273751	K562	blood:	n/a	n/a
29	HEY1	chr6:13272744-13273915	K562	blood:	n/a	chr6:13272899-13272908
30	POLR2A	chr6:13273377-13273866	GM12891	blood:	n/a	n/a
31	RELA	chr6:13272249-13275025	GM19193	blood:	n/a	n/a
32	POLR2A	chr6:13272496-13275011	GM19099	blood:	n/a	n/a
33	RELA	chr6:13272415-13276072	GM10847	blood:	n/a	n/a
34	MXI1	chr6:13272866-13273916	K562	blood:	n/a	n/a
35	TBL1XR1	chr6:13272326-13274866	GM12878	blood:	n/a	n/a
36	CUX1	chr6:13273092-13274705	K562	blood:	n/a	n/a
37	MAX	chr6:13273475-13273787	K562	blood:	n/a	n/a
38	EP300	chr6:13273394-13273995	K562	blood:	n/a	n/a
39	POLR2A	chr6:13272223-13276600	GM12878	blood:	n/a	n/a
40	MAFK	chr6:13272866-13273737	K562	blood:	n/a	n/a
41	POLR2A	chr6:13272865-13274072	PBDE	blood:	n/a	n/a
42	NR2F2	chr6:13272645-13276785	K562	blood:	n/a	n/a
43	TBL1XR1	chr6:13273325-13275040	K562	blood:	n/a	n/a
44	NR2F2	chr6:13272731-13273799	K562	blood:	n/a	n/a
45	SIN3A	chr6:13273387-13273779	GM12878	blood:	n/a	n/a
46	PML	chr6:13272251-13275171	GM12878	blood:	n/a	n/a
47	RUNX3	chr6:13272292-13274947	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:13272237-13275957	GM12892	blood:	n/a	n/a
49	POLR2A	chr6:13272526-13275090	GM18505	blood:	n/a	n/a
50	MYC	chr6:13272462-13274998	K562	blood:	n/a	chr6:13272870-13272880

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13268970..13278598-chr6:13326296..13332818,15	K562	blood:
2	chr6:13273285..13276286-chr6:13486162..13489029,4	K562	blood:
3	chr6:13273285..13276286-chr6:13486162..13489029,3	K562	blood:
4	chr6:13272896..13275816-chr6:13711430..13713666,2	K562	blood:
5	chr6:13272205..13274313-chr6:13327989..13330165,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GFOD1-1	chr6:13273623-13273738	ENSG00000215022.2

No data

Variant related genes	Relation type
PHACTR1	TF binding region
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000010017	Chromatin interaction
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1512414	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs1550526	0.83[CEU][hapmap]
rs2002961	0.85[JPT][hapmap]
rs202030	0.83[CEU][hapmap]
rs202038	0.83[CEU][hapmap]
rs202040	0.83[CEU][hapmap]
rs202042	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs202044	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs202045	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs202046	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs202051	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs202070	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs202071	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs202072	1.00[CEU][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs202073	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs202077	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2119485	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs375661	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs377704	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs3817735	0.84[JPT][hapmap]
rs3857594	0.85[JPT][hapmap]
rs405078	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs413120	1.00[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs441213	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs445591	0.86[EUR][1000 genomes]
rs445714	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs454563	0.83[CEU][hapmap]
rs4602719	0.83[CEU][hapmap]
rs495895	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6909879	0.85[JPT][hapmap]
rs7755309	0.85[JPT][hapmap]
rs8541	0.83[CEU][hapmap]
rs878700	0.85[JPT][hapmap]
rs909508	0.85[JPT][hapmap]
rs9296641	0.85[JPT][hapmap]
rs9296642	0.85[JPT][hapmap]
rs9369978	0.85[JPT][hapmap]
rs9473908	0.83[JPT][hapmap]
rs9473909	0.85[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs202053	EDN1	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
2	chr6:13256600-13278200	Weak transcription	Pancreas	Pancrea
3	chr6:13267000-13274200	Weak transcription	Gastric	stomach
4	chr6:13267400-13280400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:13267400-13283600	Weak transcription	Fetal Brain Female	brain
6	chr6:13268000-13278800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:13268000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:13269200-13282000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:13269400-13274200	Weak transcription	Aorta	Aorta
10	chr6:13269400-13275400	Weak transcription	Right Ventricle	heart
11	chr6:13269400-13284800	Weak transcription	Right Atrium	heart
12	chr6:13269600-13275600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:13269600-13286600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:13269600-13286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:13270200-13273800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:13270200-13291600	Weak transcription	HSMM	muscle
17	chr6:13270400-13282000	Weak transcription	Ovary	ovary
18	chr6:13270400-13285400	Weak transcription	Fetal Heart	heart
19	chr6:13270600-13281000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr6:13270600-13283600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
22	chr6:13272000-13273800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr6:13272000-13274000	Enhancers	Brain Substantia Nigra	brain
24	chr6:13272000-13275800	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr6:13272200-13274400	Enhancers	Brain Anterior Caudate	brain
26	chr6:13272200-13274400	Enhancers	Brain Cingulate Gyrus	brain
27	chr6:13272200-13275800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr6:13272200-13276200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr6:13272400-13274000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:13272400-13275600	Enhancers	Placenta	Placenta
31	chr6:13272400-13275600	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr6:13272400-13276600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:13272600-13274000	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr6:13272600-13274800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr6:13272600-13275200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:13272600-13275600	Active TSS	Rectal Smooth Muscle	rectum
37	chr6:13272800-13274400	Active TSS	Primary B cells from peripheral blood	blood
38	chr6:13272800-13274400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr6:13272800-13274800	Enhancers	Fetal Thymus	thymus
40	chr6:13272800-13275400	Weak transcription	Spleen	Spleen
41	chr6:13273000-13273800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:13273000-13273800	Enhancers	Brain Angular Gyrus	brain
43	chr6:13273000-13274000	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr6:13273000-13274000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr6:13273000-13274800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:13273000-13274800	Active TSS	Duodenum Mucosa	Duodenum
47	chr6:13273000-13275000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr6:13273000-13275000	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr6:13273000-13275000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:13273000-13275400	Active TSS	GM12878-XiMat	blood

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