Variant report

Variant	rs9257463
Chromosome Location	chr6:28979783-28979784
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28948083..28951244-chr6:28977635..28980493,3	K562	blood:
2	chr6:28978104..28979854-chr6:28982165..28984128,2	K562	blood:
3	chr6:28919130..28921907-chr6:28978530..28981244,2	K562	blood:
4	chr6:28944682..28947238-chr6:28977191..28980224,3	K562	blood:
5	chr6:28838242..28841047-chr6:28977615..28980299,2	MCF-7	breast:
6	chr6:28863386..28867315-chr6:28979087..28981083,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263426	Chromatin interaction
ENSG00000224157	Chromatin interaction

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

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

rs_ID	r²[population]
rs2394513	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28895350	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41316629	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41317419	0.83[AFR][1000 genomes]
rs41317427	0.83[AFR][1000 genomes]
rs6916923	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7744086	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7754810	0.81[AFR][1000 genomes]
rs9257440	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9257442	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257444	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257446	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257448	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257452	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257453	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257454	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257456	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257460	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9257469	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
13	nsv1023028	chr6:28956136-29343575	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv538170	chr6:28956136-29343575	ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
15	nsv1018937	chr6:28956136-29366175	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
16	nsv1032468	chr6:28968930-29155749	Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28978800-28979800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:28978800-28979800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:28978800-28979800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:28978800-28979800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:28978800-28979800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:28978800-28979800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:28978800-28979800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:28978800-28979800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:28978800-28979800	Active TSS	Stomach Smooth Muscle	stomach
10	chr6:28979000-28979800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:28979000-28979800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:28979000-28979800	Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr6:28979000-28979800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:28979000-28979800	Active TSS	Fetal Brain Female	brain
15	chr6:28979000-28979800	Active TSS	Ovary	ovary
16	chr6:28979000-28980000	Active TSS	Brain Germinal Matrix	brain
17	chr6:28979200-28979800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr6:28979200-28979800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr6:28979200-28979800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr6:28979400-28979800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:28979400-28979800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
22	chr6:28979400-28979800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
23	chr6:28979400-28979800	Enhancers	NHEK	skin
24	chr6:28979400-28980000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr6:28979400-28980000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:28979400-28980000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
27	chr6:28979400-28980000	Active TSS	Brain Hippocampus Middle	brain
28	chr6:28979400-28980200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
29	chr6:28979400-28980400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:28979400-28982400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:28979400-28982600	Weak transcription	Gastric	stomach
32	chr6:28979400-28982600	Weak transcription	Lung	lung
33	chr6:28979400-28982600	Weak transcription	Spleen	Spleen
34	chr6:28979600-28979800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:28979600-28979800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
36	chr6:28979600-28979800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr6:28979600-28979800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr6:28979600-28979800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
39	chr6:28979600-28979800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
40	chr6:28979600-28979800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
41	chr6:28979600-28979800	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
42	chr6:28979600-28979800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:28979600-28979800	Enhancers	Fetal Brain Male	brain
44	chr6:28979600-28979800	Flanking Active TSS	K562	blood
45	chr6:28979600-28980000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr6:28979600-28980000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
47	chr6:28979600-28980200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:28979600-28980200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:28979600-28980200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
50	chr6:28979600-28982200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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