Variant report

Variant	rs28409746
Chromosome Location	chr1:154305843-154305844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154154470..154156180-chr1:154303921..154306139,2	MCF-7	breast:
2	chr1:154294680..154296591-chr1:154305347..154307024,2	K562	blood:
3	chr1:154192531..154195371-chr1:154305230..154308167,3	MCF-7	breast:
4	chr1:154153078..154156691-chr1:154305231..154310554,8	MCF-7	breast:
5	chr1:154193867..154196410-chr1:154304631..154306238,2	K562	blood:

Variant related genes	Relation type
ENSG00000143569	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000143612	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10908831	0.95[ASN][1000 genomes]
rs11265604	0.87[ASN][1000 genomes]
rs11578607	0.87[EUR][1000 genomes]
rs11581043	0.86[EUR][1000 genomes]
rs1194584	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1194585	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1194586	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1194587	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1194592	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1194607	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1194608	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12029292	0.88[ASN][1000 genomes]
rs12033720	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1685606	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1685634	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1685635	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1760794	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1760795	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1889312	0.82[ASN][1000 genomes]
rs2483712	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2633433	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34870927	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4103781	0.87[EUR][1000 genomes]
rs72696290	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv523934	chr1:154296076-154307630	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154301000-154308400	Weak transcription	Fetal Kidney	kidney
2	chr1:154301400-154318400	Weak transcription	Small Intestine	intestine
3	chr1:154301800-154306800	Weak transcription	Right Atrium	heart
4	chr1:154301800-154307400	Weak transcription	Pancreas	Pancrea
5	chr1:154302000-154306800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:154302200-154312200	Weak transcription	Gastric	stomach
7	chr1:154302200-154312600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:154302200-154322400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:154302400-154306000	Strong transcription	NHLF	lung
10	chr1:154302400-154306400	Weak transcription	Liver	Liver
11	chr1:154302400-154306400	Strong transcription	NHDF-Ad	bronchial
12	chr1:154302400-154322400	Strong transcription	Dnd41	blood
13	chr1:154302400-154323200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:154302600-154306200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:154302600-154306200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:154302600-154306400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:154302600-154306400	Strong transcription	Stomach Smooth Muscle	stomach
18	chr1:154302600-154306600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:154302600-154307000	Strong transcription	Fetal Stomach	stomach
20	chr1:154302600-154309800	Weak transcription	Fetal Brain Male	brain
21	chr1:154302600-154314400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:154302600-154318200	Weak transcription	Fetal Heart	heart
23	chr1:154302600-154320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:154302600-154322600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:154302600-154323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:154302800-154306600	Strong transcription	Osteobl	bone
27	chr1:154302800-154307600	Strong transcription	Aorta	Aorta
28	chr1:154302800-154307800	Strong transcription	Brain Germinal Matrix	brain
29	chr1:154302800-154323000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:154303000-154306400	Strong transcription	Brain Substantia Nigra	brain
31	chr1:154303000-154306600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:154303000-154306800	Strong transcription	Brain Anterior Caudate	brain
33	chr1:154303000-154306800	Strong transcription	Brain Hippocampus Middle	brain
34	chr1:154303000-154313000	Weak transcription	Colonic Mucosa	Colon
35	chr1:154303000-154322200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:154303000-154322600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:154303200-154306600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:154303200-154306600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:154303200-154306600	Strong transcription	Fetal Muscle Leg	muscle
40	chr1:154303200-154307000	Strong transcription	Spleen	Spleen
41	chr1:154303200-154312800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:154303200-154322200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:154303200-154322400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:154303200-154323400	Strong transcription	Fetal Brain Female	brain
45	chr1:154303200-154324600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr1:154303400-154306600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:154303400-154306600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:154303400-154307000	Strong transcription	Brain Cingulate Gyrus	brain
49	chr1:154303400-154307000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr1:154303400-154307000	Strong transcription	Fetal Thymus	thymus

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