Variant report

Variant	rs9257448
Chromosome Location	chr6:28952881-28952882
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	POLR2A	chr6:28952422-28953845	Hela-S3	cervix:	n/a	n/a
2	E2F4	chr6:28952569-28953580	MCF10A-Er-Src	breast:	n/a	n/a
3	HCFC1	chr6:28952556-28953794	Hela-S3	cervix:	n/a	n/a
4	STAT3	chr6:28952818-28953481	MCF10A-Er-Src	breast:	n/a	chr6:28953168-28953176 chr6:28953176-28953184 chr6:28953248-28953262 chr6:28952927-28952938 chr6:28953251-28953260 chr6:28953250-28953259 chr6:28953249-28953260
5	GTF3C2	chr6:28952575-28953291	Hela-S3	cervix:	n/a	n/a
6	SP2	chr6:28952845-28953881	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr6:28952831-28953786	MCF10A-Er-Src	breast:	n/a	chr6:28953583-28953593 chr6:28953441-28953451
8	POLR2A	chr6:28952847-28954057	H1-hESC	embryonic stem cell:	n/a	n/a
9	STAT3	chr6:28952789-28953479	MCF10A-Er-Src	breast:	n/a	chr6:28953168-28953176 chr6:28953176-28953184 chr6:28953248-28953262 chr6:28952927-28952938 chr6:28953251-28953260 chr6:28953250-28953259 chr6:28953249-28953260
10	YY1	chr6:28952692-28953056	H1-hESC	embryonic stem cell:	n/a	n/a
11	GTF2F1	chr6:28952735-28953563	Hela-S3	cervix:	n/a	n/a
12	FOS	chr6:28952837-28953426	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr6:28952855-28953501	MCF10A-Er-Src	breast:	n/a	chr6:28953168-28953176 chr6:28953176-28953184 chr6:28953248-28953262 chr6:28952927-28952938 chr6:28953251-28953260 chr6:28953250-28953259 chr6:28953249-28953260
14	FOXA1	chr6:28952865-28953564	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28948706..28953416-chr6:28959003..28967079,12	K562	blood:
2	chr12:57480348..57481272-chr6:28952792..28953753,2	Hela-S3	cervix:
3	chr6:28952766..28954746-chr6:28971481..28973784,3	MCF-7	breast:
4	chr6:28677880..28679993-chr6:28950394..28952978,2	K562	blood:
5	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
6	chr6:28861427..28869364-chr6:28946251..28954176,23	K562	blood:
7	chr6:28805369..28807414-chr6:28949591..28952908,4	K562	blood:
8	chr6:28890052..28891752-chr6:28950586..28953290,2	MCF-7	breast:
9	chr6:28861427..28866893-chr6:28947878..28954176,14	K562	blood:
10	chr6:28889573..28894329-chr6:28949030..28952998,8	K562	blood:
11	chr6:28948241..28954799-chr6:28970209..28976187,12	MCF-7	breast:
12	chr6:28889368..28892748-chr6:28952347..28956108,5	MCF-7	breast:

Variant related genes	Relation type
HCG16	TF binding region
HCG15	TF binding region
ENSG00000225173	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000204709	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2394513	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28895350	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41316629	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41317419	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs41317427	0.88[AFR][1000 genomes]
rs6916923	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744086	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754810	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9257440	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257442	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257444	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257452	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257453	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257454	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257456	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257460	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257463	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257469	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1023540	chr6:28922691-29326018	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538169	chr6:28922691-29326018	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv869541	chr6:28922692-29326017	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv916439	chr6:28922697-29326087	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv462668	chr6:28922719-29342775	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv601213	chr6:28922719-29342775	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv1015796	chr6:28923980-29342825	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv462669	chr6:28936556-29337500	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv601214	chr6:28936556-29337500	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv601215	chr6:28946920-29348297	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28948600-28954800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:28950000-28953400	Weak transcription	Lung	lung
3	chr6:28950000-28953600	Weak transcription	Spleen	Spleen
4	chr6:28950400-28953400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:28950600-28953200	Weak transcription	Esophagus	oesophagus
6	chr6:28950600-28953200	Weak transcription	Pancreas	Pancrea
7	chr6:28950800-28953000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:28950800-28953000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:28950800-28953000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:28950800-28954200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:28951000-28953000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:28951000-28955800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:28951000-28956000	Weak transcription	GM12878-XiMat	blood
14	chr6:28951200-28953000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:28951200-28953000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:28951800-28953000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr6:28951800-28953600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:28952000-28953800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr6:28952000-28953800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:28952000-28953800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:28952000-28953800	Active TSS	Fetal Intestine Small	intestine
22	chr6:28952000-28953800	Active TSS	HMEC	breast
23	chr6:28952000-28954000	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr6:28952000-28954200	Active TSS	Brain Anterior Caudate	brain
25	chr6:28952000-28954400	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr6:28952000-28954400	Active TSS	Brain Cingulate Gyrus	brain
27	chr6:28952200-28953600	Active TSS	Duodenum Mucosa	Duodenum
28	chr6:28952200-28953600	Active TSS	Fetal Brain Male	brain
29	chr6:28952200-28953600	Active TSS	Fetal Muscle Leg	muscle
30	chr6:28952200-28953800	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr6:28952200-28953800	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr6:28952200-28953800	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr6:28952200-28953800	Active TSS	Fetal Intestine Large	intestine
34	chr6:28952200-28953800	Active TSS	Fetal Lung	lung
35	chr6:28952200-28953800	Active TSS	Fetal Stomach	stomach
36	chr6:28952200-28953800	Active TSS	Ovary	ovary
37	chr6:28952200-28953800	Active TSS	Psoas Muscle	Psoas
38	chr6:28952200-28953800	Active TSS	Right Atrium	heart
39	chr6:28952200-28953800	Active TSS	NHDF-Ad	bronchial
40	chr6:28952200-28953800	Active TSS	NHEK	skin
41	chr6:28952200-28954000	Active TSS	Muscle Satellite Cultured Cells	--
42	chr6:28952200-28954000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:28952200-28954000	Active TSS	Brain Germinal Matrix	brain
44	chr6:28952200-28954000	Active TSS	Right Ventricle	heart
45	chr6:28952200-28954200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr6:28952200-28954200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:28952200-28954200	Active TSS	Rectal Smooth Muscle	rectum
48	chr6:28952400-28953600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:28952400-28953600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:28952400-28953600	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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