Variant report

Variant	rs9381287
Chromosome Location	chr6:44040640-44040641
allele	C/G
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	PML	chr6:44040438-44041276	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:44040530-44041431	GM19193	blood:	n/a	n/a
3	RCOR1	chr6:44040445-44041119	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:44040524-44041281	GM12892	blood:	n/a	n/a
5	CUX1	chr6:44040531-44040810	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:44040590-44042516	GM12878	blood:	n/a	n/a
7	MYBL2	chr6:44040277-44043494	HepG2	liver:	n/a	chr6:44041584-44041599
8	ZMIZ1	chr6:44040511-44041116	K562	blood:	n/a	n/a
9	IRF1	chr6:44040500-44041221	K562	blood:	n/a	chr6:44040983-44040997 chr6:44040814-44040827 chr6:44040814-44040828 chr6:44040816-44040830 chr6:44040815-44040827 chr6:44040814-44040827 chr6:44040812-44040826 chr6:44040686-44040700 chr6:44040816-44040826 chr6:44040813-44040827 chr6:44040815-44040827 chr6:44040816-44040827 chr6:44040690-44040701 chr6:44040814-44040827 chr6:44040817-44040828 chr6:44040815-44040832
10	TCF7L2	chr6:44040161-44041750	HCT-116	colon:	n/a	chr6:44041105-44041119
11	MXI1	chr6:44040611-44041743	GM12878	blood:	n/a	n/a
12	FOS	chr6:44040487-44040924	MCF10A-Er-Src	breast:	n/a	n/a
13	TCF7L2	chr6:44040559-44041306	PANC-1	pancreas:	n/a	chr6:44041105-44041119
14	POLR2A	chr6:44040211-44044217	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:44040134-44043640	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:44040311-44041287	GM12878	blood:	n/a	n/a
17	MAX	chr6:44040486-44042679	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:44040490-44042590	K562	blood:	n/a	n/a
19	EP300	chr6:44040631-44041094	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:44040321-44041942	HCT-116	colon:	n/a	n/a
21	ELK1	chr6:44040532-44040955	GM12878	blood:	n/a	n/a
22	RAD21	chr6:44040297-44045355	SK-N-SH	brain:	n/a	chr6:44043089-44043098 chr6:44043985-44043998 chr6:44040377-44040387 chr6:44041243-44041257
23	MAX	chr6:44040564-44041251	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr6:44040440-44042570	Raji	blood:	n/a	n/a
25	POLR2A	chr6:44039235-44042834	U87	brain:	n/a	n/a
26	POLR2A	chr6:44040339-44042633	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr6:44040402-44041600	K562	blood:	n/a	n/a
28	POLR2A	chr6:44040454-44042530	K562	blood:	n/a	n/a
29	NRF1	chr6:44040594-44042719	SK-N-SH	brain:	n/a	chr6:44041127-44041138 chr6:44041154-44041165
30	EBF1	chr6:44040389-44040953	GM12878	blood:	n/a	chr6:44040659-44040668 chr6:44040658-44040669 chr6:44040658-44040668 chr6:44040659-44040668 chr6:44040657-44040670 chr6:44040602-44040611
31	POLR2A	chr6:44040480-44042593	GM12892	blood:	n/a	n/a
32	STAT3	chr6:44040534-44040769	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr6:44040243-44041417	GM12892	blood:	n/a	n/a
34	SRF	chr6:44040637-44040794	GM12878	blood:	n/a	chr6:44040727-44040741 chr6:44040723-44040740 chr6:44040727-44040736 chr6:44040725-44040738 chr6:44040726-44040743 chr6:44040724-44040739 chr6:44040727-44040738 chr6:44040725-44040736 chr6:44040723-44040741 chr6:44040726-44040737 chr6:44040722-44040740
35	POLR2A	chr6:44040063-44047982	HepG2	liver:	n/a	n/a
36	HEY1	chr6:44040095-44051472	HepG2	liver:	n/a	chr6:44041314-44041329 chr6:44050861-44050870
37	BHLHE40	chr6:44040619-44042614	GM12878	blood:	n/a	chr6:44041310-44041326 chr6:44041357-44041373
38	MTA3	chr6:44040444-44041039	GM12878	blood:	n/a	n/a
39	ZNF143	chr6:44040504-44041825	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:44040073-44047975	HepG2	liver:	n/a	n/a
41	RUNX3	chr6:44040637-44041112	GM12878	blood:	n/a	n/a
42	TBL1XR1	chr6:44040599-44041048	GM12878	blood:	n/a	n/a
43	ZKSCAN1	chr6:44040470-44041187	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr6:44040530-44041227	GM12891	blood:	n/a	n/a
45	MAZ	chr6:44040552-44041611	Hela-S3	cervix:	n/a	n/a
46	CHD2	chr6:44040499-44041659	GM12878	blood:	n/a	n/a
47	POLR2A	chr6:44040036-44042869	GM12878	blood:	n/a	n/a
48	EBF1	chr6:44040293-44041466	GM12878	blood:	n/a	chr6:44040659-44040668 chr6:44040658-44040669 chr6:44040658-44040668 chr6:44040659-44040668 chr6:44040657-44040670 chr6:44040602-44040611
49	NRF1	chr6:44040464-44041586	GM12878	blood:	n/a	chr6:44041127-44041138 chr6:44041154-44041165
50	STAT5A	chr6:44040472-44041078	GM12878	blood:	n/a	chr6:44040816-44040827

No.	Distal block	Cell Line	Cell type
1	chr6:43745073..43748024-chr6:44039738..44042379,2	K562	blood:
2	chr6:44031220..44034616-chr6:44038681..44041085,3	MCF-7	breast:
3	chr6:43736197..43742093-chr6:44038080..44048969,27	MCF-7	breast:
4	chr6:43736340..43742918-chr6:44039360..44044949,13	MCF-7	breast:
5	chr6:44014673..44017643-chr6:44037999..44040653,2	MCF-7	breast:
6	chr6:44040495..44042700-chr6:44055821..44057827,2	K562	blood:
7	chr6:43961901..43965076-chr6:44038380..44041329,3	MCF-7	breast:
8	chr6:44039377..44041251-chr6:44214380..44216873,3	MCF-7	breast:
9	chr6:44026622..44029059-chr6:44038076..44041600,3	MCF-7	breast:
10	chr6:44040622..44046991-chr6:44213898..44218144,6	K562	blood:
11	chr6:43730164..43744120-chr6:44034600..44052665,50	K562	blood:
12	chr6:43703640..43705628-chr6:44040199..44042446,2	K562	blood:
13	chr6:43595074..43599427-chr6:44040317..44042824,5	K562	blood:
14	chr6:44021804..44024642-chr6:44039251..44041527,2	MCF-7	breast:
15	chr6:43736441..43745894-chr6:44037513..44049664,39	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPL14-4	chr6:44036825-44041054	NONHSAT112941

Variant related genes	Relation type
ENSG00000231881	TF binding region
ENSG00000112715	Chromatin interaction
ENSG00000236961	Chromatin interaction
ENSG00000124688	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000172432	Chromatin interaction
ENSG00000272114	Chromatin interaction
ENSG00000183239	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10948121	1.00[AFR][1000 genomes]
rs12191873	1.00[AFR][1000 genomes]
rs12202501	1.00[AFR][1000 genomes]
rs12206795	1.00[AFR][1000 genomes]
rs13210320	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2064639	1.00[AFR][1000 genomes]
rs2064640	1.00[AFR][1000 genomes]
rs2092870	1.00[AFR][1000 genomes]
rs2236061	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3734697	1.00[AFR][1000 genomes]
rs4628095	1.00[AFR][1000 genomes]
rs4711764	1.00[AFR][1000 genomes]
rs4711766	1.00[AFR][1000 genomes]
rs4714738	1.00[AFR][1000 genomes]
rs4714750	1.00[AFR][1000 genomes]
rs4714754	1.00[AFR][1000 genomes]
rs4714759	1.00[AFR][1000 genomes]
rs62401766	1.00[AFR][1000 genomes]
rs62403186	0.97[EUR][1000 genomes]
rs62403189	1.00[AFR][1000 genomes]
rs9349270	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9349271	1.00[AFR][1000 genomes]
rs9349272	0.82[CHB][hapmap];1.00[AFR][1000 genomes]
rs9349275	1.00[AFR][1000 genomes]
rs9357432	1.00[AFR][1000 genomes]
rs9369448	0.82[CHB][hapmap];1.00[AFR][1000 genomes]
rs9369449	1.00[AFR][1000 genomes]
rs9369450	1.00[AFR][1000 genomes]
rs9369453	1.00[AFR][1000 genomes]
rs9369454	1.00[AFR][1000 genomes]
rs9369457	1.00[AFR][1000 genomes]
rs9381286	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9381294	1.00[AFR][1000 genomes]
rs9394984	1.00[AFR][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	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44030000-44040800	Weak transcription	Gastric	stomach
2	chr6:44037800-44040800	Weak transcription	Aorta	Aorta
3	chr6:44039000-44040800	Enhancers	NH-A	brain
4	chr6:44039000-44043600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:44040000-44040800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:44040000-44041000	Flanking Active TSS	GM12878-XiMat	blood
7	chr6:44040000-44041000	Flanking Active TSS	K562	blood
8	chr6:44040000-44041400	Enhancers	Fetal Brain Male	brain
9	chr6:44040000-44043400	Enhancers	Placenta Amnion	Placenta Amnion
10	chr6:44040200-44040800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:44040200-44040800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:44040200-44040800	Enhancers	Esophagus	oesophagus
13	chr6:44040200-44040800	Enhancers	Lung	lung
14	chr6:44040200-44040800	Enhancers	Pancreas	Pancrea
15	chr6:44040200-44041000	Flanking Active TSS	Dnd41	blood
16	chr6:44040200-44041000	Flanking Active TSS	Hela-S3	cervix
17	chr6:44040200-44041000	Flanking Active TSS	NHEK	skin
18	chr6:44040200-44041200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:44040200-44041400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:44040200-44042800	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr6:44040200-44045400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:44040400-44040800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:44040400-44040800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:44040400-44040800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:44040400-44040800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr6:44040400-44040800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr6:44040400-44040800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:44040400-44040800	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr6:44040400-44040800	Enhancers	Psoas Muscle	Psoas
30	chr6:44040400-44040800	Flanking Active TSS	Spleen	Spleen
31	chr6:44040400-44041000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
32	chr6:44040400-44041000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:44040400-44041000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr6:44040400-44041000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr6:44040400-44041000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:44040400-44041000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr6:44040400-44041000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:44040400-44041000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:44040400-44041000	Flanking Active TSS	Fetal Muscle Trunk	muscle
40	chr6:44040400-44041000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr6:44040400-44041000	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr6:44040400-44041000	Flanking Active TSS	HSMM	muscle
43	chr6:44040400-44041200	Flanking Active TSS	HMEC	breast
44	chr6:44040400-44041400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:44040400-44041400	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr6:44040400-44041600	Weak transcription	Small Intestine	intestine
47	chr6:44040400-44041800	Active TSS	H9 Cell Line	embryonic stem cell
48	chr6:44040600-44040800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:44040600-44040800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr6:44040600-44040800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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