Variant report

Variant	rs202054
Chromosome Location	chr6:13273318-13273319
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	CHD2	chr6:13272402-13273404	GM12878	blood:	n/a	n/a
2	ARID3A	chr6:13272972-13275162	K562	blood:	n/a	n/a
3	POLR2A	chr6:13272680-13275076	K562	blood:	n/a	n/a
4	MTA3	chr6:13272472-13275024	GM12878	blood:	n/a	n/a
5	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
6	ZMIZ1	chr6:13272751-13273735	K562	blood:	n/a	n/a
7	MAZ	chr6:13272420-13273362	GM12878	blood:	n/a	chr6:13272870-13272880
8	MAFF	chr6:13273043-13273937	K562	blood:	n/a	n/a
9	TBP	chr6:13272787-13273735	K562	blood:	n/a	n/a
10	MYC	chr6:13272686-13275149	K562	blood:	n/a	chr6:13272870-13272880
11	MAX	chr6:13272344-13273697	NB4	blood:	n/a	chr6:13272870-13272880
12	JUN	chr6:13272018-13276804	K562	blood:	n/a	chr6:13276647-13276657
13	POLR2A	chr6:13272688-13273666	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:13273189-13273763	GM12891	blood:	n/a	n/a
15	IRF1	chr6:13273314-13273961	K562	blood:	n/a	n/a
16	RELA	chr6:13272294-13275127	GM12891	blood:	n/a	n/a
17	POLR2A	chr6:13271984-13273855	K562	blood:	n/a	n/a
18	HEY1	chr6:13272744-13273915	K562	blood:	n/a	chr6:13272899-13272908
19	RELA	chr6:13272249-13275025	GM19193	blood:	n/a	n/a
20	NFIC	chr6:13272658-13273319	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:13272496-13275011	GM19099	blood:	n/a	n/a
22	RELA	chr6:13272415-13276072	GM10847	blood:	n/a	n/a
23	MXI1	chr6:13272866-13273916	K562	blood:	n/a	n/a
24	TBL1XR1	chr6:13272326-13274866	GM12878	blood:	n/a	n/a
25	CUX1	chr6:13273092-13274705	K562	blood:	n/a	n/a
26	POLR2A	chr6:13272223-13276600	GM12878	blood:	n/a	n/a
27	MAFK	chr6:13272866-13273737	K562	blood:	n/a	n/a
28	POLR2A	chr6:13272865-13274072	PBDE	blood:	n/a	n/a
29	NR2F2	chr6:13272645-13276785	K562	blood:	n/a	n/a
30	NR2F2	chr6:13272731-13273799	K562	blood:	n/a	n/a
31	PML	chr6:13272251-13275171	GM12878	blood:	n/a	n/a
32	RELA	chr6:13272819-13273410	GM18505	blood:	n/a	n/a
33	RUNX3	chr6:13272292-13274947	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:13272237-13275957	GM12892	blood:	n/a	n/a
35	POLR2A	chr6:13272526-13275090	GM18505	blood:	n/a	n/a
36	MYC	chr6:13272462-13274998	K562	blood:	n/a	chr6:13272870-13272880
37	ATF2	chr6:13272505-13273506	GM12878	blood:	n/a	n/a
38	MXI1	chr6:13272324-13275420	GM12878	blood:	n/a	n/a
39	STAT5A	chr6:13272382-13275170	GM12878	blood:	n/a	chr6:13272427-13272439
40	MAX	chr6:13272386-13273765	GM12878	blood:	n/a	chr6:13272870-13272880
41	TEAD4	chr6:13272318-13275177	K562	blood:	n/a	n/a
42	HCFC1	chr6:13272799-13273966	K562	blood:	n/a	n/a
43	MEF2A	chr6:13272737-13273326	GM12878	blood:	n/a	chr6:13272928-13272936
44	BHLHE40	chr6:13272222-13275037	GM12878	blood:	n/a	chr6:13272899-13272908 chr6:13272899-13272908 chr6:13272900-13272909 chr6:13272874-13272890 chr6:13272849-13272865 chr6:13272893-13272914
45	PML	chr6:13272714-13273955	K562	blood:	n/a	n/a
46	POLR2A	chr6:13271496-13276674	K562	blood:	n/a	n/a
47	POLR2A	chr6:13272368-13276162	GM12878	blood:	n/a	n/a
48	MTA3	chr6:13272032-13276170	GM12878	blood:	n/a	n/a
49	GATA1	chr6:13273306-13274004	PBDE	blood:	n/a	n/a
50	MYC	chr6:13272743-13274626	K562	blood:	n/a	chr6:13272870-13272880

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:

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

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1937767	0.82[CEU][hapmap]
rs202039	0.84[CEU][hapmap]
rs202066	0.86[CEU][hapmap]
rs3846903	0.81[JPT][hapmap]
rs384730	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs412787	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs417048	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs421057	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs442614	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs202054	GFOD1	cis	lymphoblastoid	seeQTL
rs202054	ERVFRDE1	cis	cerebellum	SCAN

Chromatin state (count:74 , 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	chr6:13270800-13273400	Weak transcription	HSMMtube	muscle
22	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
23	chr6:13272000-13273800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr6:13272000-13274000	Enhancers	Brain Substantia Nigra	brain
25	chr6:13272000-13275800	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr6:13272200-13273400	Strong transcription	Brain Germinal Matrix	brain
27	chr6:13272200-13274400	Enhancers	Brain Anterior Caudate	brain
28	chr6:13272200-13274400	Enhancers	Brain Cingulate Gyrus	brain
29	chr6:13272200-13275800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr6:13272200-13276200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr6:13272400-13273400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr6:13272400-13273400	Transcr. at gene 5' and 3'	K562	blood
33	chr6:13272400-13274000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:13272400-13275600	Enhancers	Placenta	Placenta
35	chr6:13272400-13275600	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr6:13272400-13276600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:13272600-13273400	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr6:13272600-13274000	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr6:13272600-13274800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr6:13272600-13275200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:13272600-13275600	Active TSS	Rectal Smooth Muscle	rectum
42	chr6:13272800-13273600	Enhancers	Primary T cells from cord blood	blood
43	chr6:13272800-13274400	Active TSS	Primary B cells from peripheral blood	blood
44	chr6:13272800-13274400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr6:13272800-13274800	Enhancers	Fetal Thymus	thymus
46	chr6:13272800-13275400	Weak transcription	Spleen	Spleen
47	chr6:13273000-13273400	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr6:13273000-13273400	Active TSS	Liver	Liver
49	chr6:13273000-13273600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:13273000-13273600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links