Variant report

Variant	rs6426178
Chromosome Location	chr1:224363370-224363371
allele	A/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	TAF1	chr1:224363356-224363631	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:224363260-224363756	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:224363296-224363823	MCF-7	breast:	n/a	n/a
4	POLR2A	chr1:224363166-224363818	ProgFib	skin:	n/a	n/a
5	POLR2A	chr1:224363356-224363545	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:224363365-224363623	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr1:224363334-224363643	SK-N-SH_RA	brain:	n/a	chr1:224363457-224363476
8	HEY1	chr1:224363345-224363588	K562	blood:	n/a	chr1:224363568-224363583
9	RAD21	chr1:224363365-224363610	H1-hESC	embryonic stem cell:	n/a	chr1:224363457-224363476
10	POLR2A	chr1:224363238-224363629	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr1:224363275-224363573	GM12878	blood:	n/a	n/a
12	TAF1	chr1:224363231-224363663	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:224363364-224363627	A549	lung:	n/a	n/a
14	HEY1	chr1:224363347-224363636	K562	blood:	n/a	chr1:224363568-224363583
15	MAFK	chr1:224363325-224363394	HepG2	liver:	n/a	chr1:224363369-224363384
16	CTCF	chr1:224363360-224363510	HA-sp	spinal cord:	n/a	n/a
17	POLR2A	chr1:224363359-224363616	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr1:224363340-224363490	SK-N-SH_RA	brain:	n/a	n/a
19	POLR2A	chr1:224363140-224363393	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr1:224363248-224363714	H1-hESC	embryonic stem cell:	n/a	chr1:224363457-224363476
21	POLR2A	chr1:224363215-224363709	H1-hESC	embryonic stem cell:	n/a	n/a
22	TBP	chr1:224363366-224363608	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr1:224363360-224363510	HPAF	blood vessel:	n/a	n/a
24	POLR2A	chr1:224363351-224363718	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:224363055..224364051-chr8:102217454..102218022,3	MCF-7	breast:
2	chr1:224363073..224364083-chr8:102217577..102218188,4	MCF-7	breast:
3	chr1:224362050..224363556-chr8:102216788..102219070,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NVL-6	chr1:224363178-224363408	NONHSAT009776

Variant related genes	Relation type
ENSG00000201898	TF binding region
DEGS1	TF binding region
ENSG00000120963	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10799505	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs10916301	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs10916371	0.86[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs10916415	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap]
rs12038372	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12049583	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs16844819	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap]
rs17560970	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1826421	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2011117	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs2172361	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2404843	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs2896985	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs3767730	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs3820482	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs3820483	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs4653564	0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4653568	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs4653986	0.86[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs4654003	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs6426139	0.82[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs6658494	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6659234	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs6681673	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs6682292	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs6685783	0.82[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs6688818	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs6691405	0.82[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs6700284	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs7511895	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs7518839	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs7524705	0.85[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap]
rs7526252	0.85[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap]
rs7531891	0.86[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap]
rs8328	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs869945	0.81[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs908801	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs997297	0.90[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv8857	chr1:224359943-224383023	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6426178	FBXO28	cis	multi-tissue	Pritchard
rs6426178	FBXO28	Cis_1M	lymphoblastoid	RTeQTL
rs6426178	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:224345400-224363400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:224345600-224363400	Weak transcription	Ovary	ovary
4	chr1:224346400-224370000	Weak transcription	Esophagus	oesophagus
5	chr1:224346600-224363400	Weak transcription	Right Ventricle	heart
6	chr1:224346600-224363400	Weak transcription	Spleen	Spleen
7	chr1:224357200-224363400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:224358200-224363400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:224358400-224363400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:224358600-224363400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:224358600-224363400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:224359000-224363400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:224359000-224363400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:224359000-224369200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:224359000-224369200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:224359000-224370200	Weak transcription	Small Intestine	intestine
17	chr1:224359200-224363400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:224359200-224363400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:224362600-224363800	Enhancers	Fetal Thymus	thymus
20	chr1:224362800-224369600	Weak transcription	Fetal Intestine Small	intestine
21	chr1:224363000-224363400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr1:224363000-224363800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr1:224363200-224363400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr1:224363200-224363400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
25	chr1:224363200-224363400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:224363200-224363400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:224363200-224363400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:224363200-224363400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:224363200-224363400	Enhancers	Fetal Intestine Large	intestine
30	chr1:224363200-224363400	Flanking Active TSS	NH-A	brain
31	chr1:224363200-224363600	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr1:224363200-224363600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:224363200-224363600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:224363200-224363600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr1:224363200-224363600	Active TSS	Brain Anterior Caudate	brain
36	chr1:224363200-224363600	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr1:224363200-224363600	Enhancers	Fetal Stomach	stomach
38	chr1:224363200-224363600	Enhancers	HMEC	breast
39	chr1:224363200-224363600	Enhancers	HUVEC	blood vessel
40	chr1:224363200-224363800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:224363200-224363800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:224363200-224363800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:224363200-224363800	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr1:224363200-224363800	Enhancers	Primary B cells from cord blood	blood
45	chr1:224363200-224363800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:224363200-224363800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:224363200-224363800	Active TSS	Brain Angular Gyrus	brain
48	chr1:224363200-224363800	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr1:224363200-224363800	Active TSS	Rectal Smooth Muscle	rectum
50	chr1:224363200-224363800	Flanking Active TSS	NHEK	skin

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