Variant report

Variant	rs9295782
Chromosome Location	chr6:28890219-28890220
allele	A/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	NR2F2	chr6:28889743-28892578	K562	blood:	n/a	n/a
2	POLR2A	chr6:28889875-28892268	HUVEC	blood vessel:	n/a	n/a
3	CEBPB	chr6:28889892-28890601	IMR90	lung:	n/a	n/a
4	PML	chr6:28889740-28892185	K562	blood:	n/a	chr6:28890027-28890036
5	MXI1	chr6:28889872-28892194	IMR90	lung:	n/a	n/a
6	FOSL2	chr6:28889756-28890258	HepG2	liver:	n/a	chr6:28890022-28890033 chr6:28890025-28890035 chr6:28890025-28890036 chr6:28890027-28890034 chr6:28890026-28890034 chr6:28890026-28890035 chr6:28890024-28890036
7	POLR2A	chr6:28889681-28892110	K562	blood:	n/a	n/a
8	MYC	chr6:28889855-28890544	MCF10A-Er-Src	breast:	n/a	chr6:28890440-28890449 chr6:28890026-28890035 chr6:28890025-28890034
9	POLR2A	chr6:28889280-28892096	K562	blood:	n/a	n/a
10	FOS	chr6:28889830-28890236	K562	blood:	n/a	chr6:28890022-28890033 chr6:28890025-28890035 chr6:28890027-28890034 chr6:28890026-28890034 chr6:28890026-28890035 chr6:28890024-28890036
11	FOSL2	chr6:28889842-28890275	HepG2	liver:	n/a	chr6:28890022-28890033 chr6:28890025-28890035 chr6:28890025-28890036 chr6:28890027-28890034 chr6:28890026-28890034 chr6:28890026-28890035 chr6:28890024-28890036
12	ZNF263	chr6:28889915-28892045	HEK293-T-REx	kidney:	n/a	n/a
13	POLR2A	chr6:28889873-28892186	HUVEC	blood vessel:	n/a	n/a
14	MAFK	chr6:28889927-28890593	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr6:28889258-28892112	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:28889870-28892107	PBDE	blood:	n/a	n/a
17	STAT3	chr6:28889896-28890433	MCF10A-Er-Src	breast:	n/a	chr6:28890026-28890035 chr6:28890025-28890034
18	FOSL2	chr6:28889750-28890260	A549	lung:	n/a	chr6:28890022-28890033 chr6:28890025-28890035 chr6:28890025-28890036 chr6:28890027-28890034 chr6:28890026-28890034 chr6:28890026-28890035 chr6:28890024-28890036
19	MYC	chr6:28889871-28892047	K562	blood:	n/a	chr6:28890440-28890449 chr6:28890026-28890035 chr6:28890025-28890034
20	POLR2A	chr6:28889737-28892105	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr6:28890128-28892096	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:28889355-28892105	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:28886841-28892929	HepG2	liver:	n/a	n/a
24	HEY1	chr6:28889664-28892232	HepG2	liver:	n/a	chr6:28891795-28891810 chr6:28891995-28892010
25	POLR2A	chr6:28889545-28891524	K562	blood:	n/a	n/a
26	POLR2A	chr6:28889706-28892116	GM12891	blood:	n/a	n/a
27	MAFF	chr6:28889865-28890820	K562	blood:	n/a	n/a
28	STAT1	chr6:28889757-28892100	Hela-S3	cervix:	n/a	chr6:28890026-28890035 chr6:28890025-28890034
29	USF2	chr6:28889994-28890621	HepG2	liver:	n/a	chr6:28890438-28890449
30	USF1	chr6:28890143-28890584	K562	blood:	n/a	n/a
31	EP300	chr6:28889855-28890566	K562	blood:	n/a	chr6:28890025-28890034 chr6:28890026-28890035
32	POLR2A	chr6:28889603-28892955	K562	blood:	n/a	n/a
33	JUND	chr6:28889577-28890512	Hela-S3	cervix:	n/a	chr6:28890024-28890035 chr6:28890436-28890445 chr6:28890022-28890033 chr6:28890025-28890035 chr6:28890027-28890034 chr6:28890026-28890034 chr6:28890026-28890035 chr6:28890024-28890036
34	POLR2A	chr6:28889790-28892084	HepG2	liver:	n/a	n/a
35	POLR2A	chr6:28889833-28892124	HUVEC	blood vessel:	n/a	n/a
36	FOS	chr6:28889837-28890553	MCF10A-Er-Src	breast:	n/a	chr6:28890436-28890445 chr6:28890022-28890033 chr6:28890025-28890035 chr6:28890027-28890034 chr6:28890026-28890034 chr6:28890026-28890035 chr6:28890024-28890036
37	CEBPB	chr6:28889766-28890292	MCF-7	breast:	n/a	n/a
38	FOSL2	chr6:28889774-28890291	MCF-7	breast:	n/a	chr6:28890022-28890033 chr6:28890025-28890035 chr6:28890025-28890036 chr6:28890027-28890034 chr6:28890026-28890034 chr6:28890026-28890035 chr6:28890024-28890036
39	POLR2A	chr6:28889784-28892144	GM12892	blood:	n/a	n/a
40	SIN3AK20	chr6:28889852-28892076	K562	blood:	n/a	n/a
41	JUN	chr6:28889854-28890230	K562	blood:	n/a	chr6:28890022-28890033 chr6:28890025-28890035 chr6:28890027-28890034 chr6:28890026-28890034 chr6:28890026-28890035 chr6:28890024-28890036
42	FOS	chr6:28889854-28890608	MCF10A-Er-Src	breast:	n/a	chr6:28890436-28890445 chr6:28890022-28890033 chr6:28890025-28890035 chr6:28890027-28890034 chr6:28890026-28890034 chr6:28890026-28890035 chr6:28890024-28890036
43	POLR2A	chr6:28890046-28892078	IMR90	lung:	n/a	n/a
44	MBD4	chr6:28889836-28892105	HepG2	liver:	n/a	n/a
45	MYC	chr6:28889948-28892100	A549	lung:	n/a	chr6:28890440-28890449 chr6:28890026-28890035 chr6:28890025-28890034
46	MXI1	chr6:28889811-28891923	K562	blood:	n/a	n/a
47	MAX	chr6:28889618-28890233	MCF-7	breast:	n/a	chr6:28890026-28890035 chr6:28890025-28890034
48	JUN	chr6:28889858-28890698	K562	blood:	n/a	chr6:28890436-28890445 chr6:28890022-28890033 chr6:28890025-28890035 chr6:28890027-28890034 chr6:28890026-28890034 chr6:28890026-28890035 chr6:28890024-28890036
49	E2F4	chr6:28889990-28890572	MCF10A-Er-Src	breast:	n/a	n/a
50	STAT3	chr6:28889809-28890242	MCF10A-Er-Src	breast:	n/a	chr6:28890026-28890035 chr6:28890025-28890034

No.	Distal block	Cell Line	Cell type
1	chr17:73874220..73874999-chr6:28890150..28891088,2	Hela-S3	cervix:
2	chr6:28887886..28894013-chr6:28935014..28940220,8	K562	blood:
3	chr6:28831130..28836886-chr6:28890033..28892870,9	MCF-7	breast:
4	chr6:28889368..28892748-chr6:28952347..28956108,5	MCF-7	breast:
5	chr6:28861677..28871493-chr6:28888734..28892704,20	MCF-7	breast:
6	chr6:28874441..28877573-chr6:28886876..28891614,6	MCF-7	breast:
7	chr6:28889372..28892274-chr6:28936954..28941148,4	K562	blood:
8	chr6:28889101..28891643-chr6:29595051..29597893,2	K562	blood:
9	chr6:28831640..28835125-chr6:28890004..28893108,3	MCF-7	breast:
10	chr6:28874958..28881784-chr6:28883001..28892669,21	MCF-7	breast:
11	chr6:28861810..28871966-chr6:28889574..28894668,20	MCF-7	breast:
12	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
13	chr6:28805285..28808440-chr6:28888511..28892745,5	K562	blood:
14	chr6:28886838..28893375-chr6:28904762..28912890,19	K562	blood:
15	chr6:27776463..27779000-chr6:28890031..28892525,2	MCF-7	breast:
16	chr6:28890160..28893119-chr6:28970726..28976038,6	K562	blood:
17	chr6:28804571..28808832-chr6:28889803..28892525,4	MCF-7	breast:

Variant related genes	Relation type
TRIM27	TF binding region
ENSG00000227214	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000132481	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000244349	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000204681	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000228666	Chromatin interaction
ENSG00000225173	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1041881	0.81[EUR][1000 genomes]
rs1056032	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12194037	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17399888	0.86[EUR][1000 genomes]
rs2071786	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2071787	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2071788	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28531681	0.83[EUR][1000 genomes]
rs2894065	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3763338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763339	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713180	0.81[EUR][1000 genomes]
rs4713182	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4713183	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4713184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713191	0.91[EUR][1000 genomes]
rs4713195	0.85[EUR][1000 genomes]
rs4713196	0.85[EUR][1000 genomes]
rs4947256	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61751894	0.88[EUR][1000 genomes]
rs6456865	0.80[ASN][1000 genomes]
rs6456866	0.82[ASN][1000 genomes]
rs6928948	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6936343	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72853516	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72853522	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72853523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72860085	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72860099	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72862420	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72862423	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73408958	0.82[ASN][1000 genomes]
rs73741203	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs743848	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7745220	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7746064	0.82[ASN][1000 genomes]
rs7761745	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7762289	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9366731	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9366733	0.83[EUR][1000 genomes]
rs9380098	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380100	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9380102	0.90[EUR][1000 genomes]
rs9380103	0.83[EUR][1000 genomes]
rs968723	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription 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	47 gene(s)	inside rSNPs	diseases
5	nsv462667	chr6:28834646-28893927	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28889200-28890400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:28889200-28890800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
3	chr6:28889200-28890800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
4	chr6:28889200-28890800	Transcr. at gene 5' and 3'	K562	blood
5	chr6:28889200-28891400	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr6:28889400-28890400	Enhancers	Small Intestine	intestine
7	chr6:28889400-28890400	Transcr. at gene 5' and 3'	Hela-S3	cervix
8	chr6:28889400-28890600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
9	chr6:28889400-28890600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr6:28889400-28890800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
11	chr6:28889400-28890800	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr6:28889600-28890400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:28889600-28890400	Enhancers	Esophagus	oesophagus
14	chr6:28889600-28890600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:28889600-28890600	Flanking Active TSS	Liver	Liver
16	chr6:28889600-28890600	Transcr. at gene 5' and 3'	HSMM	muscle
17	chr6:28889600-28890800	Flanking Active TSS	Fetal Brain Female	brain
18	chr6:28889800-28890400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:28889800-28890400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
20	chr6:28889800-28890400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:28889800-28890400	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr6:28889800-28890400	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
23	chr6:28889800-28890400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr6:28889800-28890400	Flanking Active TSS	Osteobl	bone
25	chr6:28889800-28890600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
26	chr6:28889800-28890600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:28889800-28890600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr6:28889800-28890600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:28889800-28890600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:28889800-28890600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr6:28889800-28890600	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr6:28889800-28890600	Flanking Active TSS	HMEC	breast
33	chr6:28889800-28890600	Flanking Active TSS	HUVEC	blood vessel
34	chr6:28889800-28890600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr6:28889800-28890800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr6:28889800-28890800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr6:28889800-28890800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr6:28889800-28890800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:28889800-28890800	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr6:28889800-28890800	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr6:28889800-28890800	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr6:28889800-28892400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:28889800-28892600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:28890000-28890400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:28890000-28890400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:28890000-28890400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:28890000-28890400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:28890000-28890400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:28890000-28890400	Flanking Active TSS	Fetal Heart	heart
50	chr6:28890000-28890400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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