Variant report

Variant	rs9257444
Chromosome Location	chr6:28948857-28948858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28948706..28953416-chr6:28959003..28967079,12	K562	blood:
2	chr6:28946686..28952098-chr6:28981757..28987491,9	K562	blood:
3	chr6:28829291..28833354-chr6:28946684..28949723,4	K562	blood:
4	chr6:28804861..28808227-chr6:28947720..28951878,5	K562	blood:
5	chr6:28907253..28915101-chr6:28945522..28952393,17	K562	blood:
6	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
7	chr6:28723907..28726622-chr6:28947645..28950512,2	K562	blood:
8	chr6:28861427..28869364-chr6:28946251..28954176,23	K562	blood:
9	chr6:28916972..28925607-chr6:28947207..28951909,14	K562	blood:
10	chr6:28829291..28833978-chr6:28947381..28950490,6	K562	blood:
11	chr6:28928142..28929743-chr6:28947588..28949383,2	K562	blood:
12	chr6:28948083..28951244-chr6:28977635..28980493,3	K562	blood:
13	chr6:28861427..28866893-chr6:28947878..28954176,14	K562	blood:
14	chr6:28889725..28893274-chr6:28947221..28952049,9	MCF-7	breast:
15	chr6:28948241..28954799-chr6:28970209..28976187,12	MCF-7	breast:
16	chr6:28888560..28894615-chr6:28945306..28952099,20	K562	blood:
17	chr6:28940964..28943621-chr6:28945663..28948952,4	K562	blood:
18	chr6:27859640..27862411-chr6:28946747..28949086,3	K562	blood:
19	chr6:28907996..28910654-chr6:28948439..28951310,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000204709	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000233224	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	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28895350	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41316629	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41317419	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs41317427	0.86[AFR][1000 genomes]
rs6916923	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744086	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754810	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9257440	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257442	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257446	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257448	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257452	0.93[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257456	0.93[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	0.88[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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28948000-28949000	Flanking Active TSS	Dnd41	blood
2	chr6:28948200-28949000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr6:28948200-28949000	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr6:28948200-28950800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:28948200-28950800	Active TSS	Brain Anterior Caudate	brain
6	chr6:28948200-28951000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr6:28948200-28951000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:28948400-28949000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:28948400-28949000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:28948400-28949000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:28948400-28949000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
12	chr6:28948400-28949000	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr6:28948400-28949000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:28948400-28949000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr6:28948400-28949000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:28948400-28949000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr6:28948400-28949000	Flanking Active TSS	HMEC	breast
18	chr6:28948400-28949000	Flanking Active TSS	HUVEC	blood vessel
19	chr6:28948400-28949000	Flanking Active TSS	NH-A	brain
20	chr6:28948400-28949000	Flanking Active TSS	NHDF-Ad	bronchial
21	chr6:28948400-28949000	Flanking Active TSS	NHEK	skin
22	chr6:28948400-28949000	Flanking Active TSS	Osteobl	bone
23	chr6:28948400-28949400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr6:28948400-28950600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:28948400-28950600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:28948400-28950600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:28948400-28950600	Active TSS	Brain Cingulate Gyrus	brain
28	chr6:28948400-28950600	Active TSS	Fetal Heart	heart
29	chr6:28948400-28950600	Active TSS	Fetal Kidney	kidney
30	chr6:28948400-28950600	Active TSS	Rectal Smooth Muscle	rectum
31	chr6:28948400-28950600	Active TSS	HSMM	muscle
32	chr6:28948400-28950800	Active TSS	H9 Cell Line	embryonic stem cell
33	chr6:28948400-28950800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:28948400-28950800	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr6:28948400-28950800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:28948400-28950800	Active TSS	Brain Germinal Matrix	brain
37	chr6:28948400-28950800	Active TSS	Brain Substantia Nigra	brain
38	chr6:28948400-28950800	Active TSS	Right Ventricle	heart
39	chr6:28948400-28950800	Active TSS	A549	lung
40	chr6:28948400-28951000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:28948400-28951000	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr6:28948400-28951000	Active TSS	Brain Hippocampus Middle	brain
43	chr6:28948400-28951000	Active TSS	Fetal Brain Female	brain
44	chr6:28948400-28951000	Active TSS	Stomach Smooth Muscle	stomach
45	chr6:28948400-28951000	Active TSS	HSMMtube	muscle
46	chr6:28948400-28951800	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr6:28948600-28949000	Flanking Active TSS	Liver	Liver
48	chr6:28948600-28949000	Flanking Active TSS	Fetal Brain Male	brain
49	chr6:28948600-28949000	Flanking Active TSS	Psoas Muscle	Psoas
50	chr6:28948600-28949000	Enhancers	Sigmoid Colon	Sigmoid Colon

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