Variant report

Variant	rs1824619
Chromosome Location	chr6:107076696-107076697
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	FOXA2	chr6:107076678-107077066	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:107076645-107078679	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:107076625-107078631	HepG2	liver:	n/a	n/a
4	RUNX3	chr6:107076613-107077910	GM12878	blood:	n/a	n/a
5	MYC	chr6:107076663-107078110	K562	blood:	n/a	n/a
6	IRF1	chr6:107076614-107076940	K562	blood:	n/a	n/a
7	MXI1	chr6:107076500-107077967	IMR90	lung:	n/a	n/a
8	SIN3A	chr6:107076665-107077783	GM12878	blood:	n/a	n/a
9	FOXA1	chr6:107076569-107077131	HepG2	liver:	n/a	chr6:107076867-107076882 chr6:107076893-107076908
10	CUX1	chr6:107076519-107077112	K562	blood:	n/a	n/a
11	IRF1	chr6:107076609-107077709	K562	blood:	n/a	chr6:107077053-107077063 chr6:107077028-107077041 chr6:107077379-107077388 chr6:107077049-107077063 chr6:107077051-107077064 chr6:107077053-107077067 chr6:107077051-107077064 chr6:107077181-107077195
12	FOXA1	chr6:107076589-107077077	HepG2	liver:	n/a	chr6:107076867-107076882 chr6:107076893-107076908
13	STAT3	chr6:107076669-107077613	GM12878	blood:	n/a	chr6:107077053-107077064
14	RUNX3	chr6:107076597-107077716	GM12878	blood:	n/a	n/a
15	PML	chr6:107076528-107078011	GM12878	blood:	n/a	n/a
16	FOXA1	chr6:107076662-107076992	T-47D	breast:	n/a	chr6:107076867-107076882 chr6:107076893-107076908
17	FOXA1	chr6:107076633-107076986	T-47D	breast:	n/a	chr6:107076867-107076882 chr6:107076893-107076908
18	POLR2A	chr6:107076286-107078697	GM12891	blood:	n/a	n/a
19	POLR2A	chr6:107076424-107076882	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr6:107076686-107077910	Raji	blood:	n/a	n/a
21	MTA3	chr6:107076581-107077372	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:107076661-107077987	K562	blood:	n/a	n/a
23	POLR2A	chr6:107076298-107078655	GM19193	blood:	n/a	n/a
24	RELA	chr6:107076658-107077645	GM19099	blood:	n/a	n/a
25	HCFC1	chr6:107076360-107078680	Hela-S3	cervix:	n/a	n/a
26	SMC3	chr6:107076666-107078232	Hela-S3	cervix:	n/a	n/a
27	MXI1	chr6:107076674-107077877	HepG2	liver:	n/a	n/a
28	STAT1	chr6:107076613-107077703	GM12878	blood:	n/a	chr6:107077053-107077064
29	POLR2A	chr6:107076669-107078398	Hela-S3	cervix:	n/a	n/a
30	NFIC	chr6:107076641-107077768	GM12878	blood:	n/a	n/a
31	ARID3A	chr6:107076556-107077379	HepG2	liver:	n/a	n/a
32	FOXA1	chr6:107076581-107077153	HepG2	liver:	n/a	chr6:107076867-107076882 chr6:107076893-107076908
33	POLR2A	chr6:107076637-107076769	MCF-7	breast:	n/a	n/a
34	EP300	chr6:107076659-107077654	GM12878	blood:	n/a	chr6:107077048-107077062
35	CUX1	chr6:107076562-107077265	GM12878	blood:	n/a	n/a
36	TBP	chr6:107076667-107077824	HepG2	liver:	n/a	n/a
37	ATF2	chr6:107076448-107077652	GM12878	blood:	n/a	n/a
38	FOXA1	chr6:107076607-107077191	HepG2	liver:	n/a	chr6:107076867-107076882 chr6:107076893-107076908
39	RELA	chr6:107076695-107077865	GM18951	blood:	n/a	n/a
40	POU2F2	chr6:107076695-107077792	GM12878	blood:	n/a	n/a
41	POLR2A	chr6:107076669-107076837	HepG2	liver:	n/a	n/a
42	MTA3	chr6:107076480-107078069	GM12878	blood:	n/a	n/a
43	MXI1	chr6:107076290-107078403	SK-N-SH	brain:	n/a	n/a
44	TBP	chr6:107076690-107077662	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr6:107076527-107078679	MCF10A-Er-Src	breast:	n/a	n/a
46	ZNF384	chr6:107076588-107077643	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:76530831..76531804-chr6:107076635..107077304,2	HCT-116	colon:
2	chr6:107074480..107076734-chr6:107196823..107198959,2	MCF-7	breast:

Variant related genes	Relation type
QRSL1	TF binding region
ENSG00000257872	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10499045	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs12110543	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12111259	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12660628	0.83[JPT][hapmap]
rs12663879	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2035152	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035153	1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035154	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2035155	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2353040	1.00[ASN][1000 genomes]
rs3747791	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3747792	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3804343	0.83[JPT][hapmap]
rs4946769	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946771	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946772	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946773	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs59238907	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6568446	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6900830	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900886	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905061	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6905519	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906495	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914497	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs6916265	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919395	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6923868	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925367	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925512	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933064	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72613231	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72613232	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72613233	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72613234	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72613235	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72613236	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72613237	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72613238	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72613241	1.00[EUR][1000 genomes]
rs7454323	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748400	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7759021	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372137	1.00[ASN][1000 genomes]
rs9373881	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:107030800-107076800	Weak transcription	Small Intestine	intestine
2	chr6:107031200-107077000	Weak transcription	Spleen	Spleen
3	chr6:107053000-107076800	Weak transcription	Esophagus	oesophagus
4	chr6:107053000-107076800	Weak transcription	Gastric	stomach
5	chr6:107070800-107076800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:107070800-107076800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:107070800-107077000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:107075800-107077000	Flanking Active TSS	Primary B cells from peripheral blood	blood
9	chr6:107075800-107077800	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr6:107076000-107077000	Flanking Active TSS	Dnd41	blood
11	chr6:107076200-107077000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:107076200-107078000	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr6:107076200-107078000	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr6:107076200-107078000	Active TSS	Rectal Smooth Muscle	rectum
15	chr6:107076200-107078400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:107076200-107079400	Active TSS	K562	blood
17	chr6:107076200-107080600	Active TSS	GM12878-XiMat	blood
18	chr6:107076400-107076800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr6:107076400-107076800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr6:107076400-107076800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:107076400-107076800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:107076400-107076800	Flanking Active TSS	Fetal Brain Male	brain
23	chr6:107076400-107076800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr6:107076400-107076800	Flanking Active TSS	Hela-S3	cervix
25	chr6:107076400-107076800	Flanking Bivalent TSS/Enh	HepG2	liver
26	chr6:107076400-107076800	Flanking Active TSS	NHEK	skin
27	chr6:107076400-107076800	Flanking Active TSS	Osteobl	bone
28	chr6:107076400-107077000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:107076400-107077000	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr6:107076400-107077000	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr6:107076400-107077000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr6:107076400-107077000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:107076400-107077000	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr6:107076400-107077000	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr6:107076400-107077000	Flanking Active TSS	Fetal Kidney	kidney
36	chr6:107076400-107077000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr6:107076400-107077200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr6:107076400-107078000	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr6:107076400-107078000	Active TSS	Brain Substantia Nigra	brain
40	chr6:107076400-107078000	Active TSS	Colon Smooth Muscle	Colon
41	chr6:107076400-107078000	Active TSS	Fetal Brain Female	brain
42	chr6:107076400-107078200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:107076400-107078200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:107076400-107078200	Active TSS	Stomach Smooth Muscle	stomach
45	chr6:107076400-107078400	Active TSS	H1 Cell Line	embryonic stem cell
46	chr6:107076400-107078400	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr6:107076400-107078400	Active TSS	Psoas Muscle	Psoas
48	chr6:107076400-107078400	Active TSS	Right Atrium	heart
49	chr6:107076400-107078400	Active TSS	HMEC	breast
50	chr6:107076400-107078400	Active TSS	HSMMtube	muscle

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