Variant report

Variant	rs6427575
Chromosome Location	chr1:154305560-154305561
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	chr1:154304058..154305639-chr19:47729768..47731392,2	K562	blood:
6	chr1:154193867..154196410-chr1:154304631..154306238,2	K562	blood:

Variant related genes	Relation type
ENSG00000143612	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000265134	Chromatin interaction
ENSG00000105327	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11265539	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11576151	0.81[AMR][1000 genomes]
rs11578377	0.92[EUR][1000 genomes]
rs11578646	0.92[EUR][1000 genomes]
rs11579790	0.92[EUR][1000 genomes]
rs11800830	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1194583	0.86[ASN][1000 genomes]
rs17699328	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1931298	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2010828	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4040747	0.90[AMR][1000 genomes]
rs56128567	0.85[EUR][1000 genomes]
rs6427568	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6673495	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6691345	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs767804	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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	chr1:154302400-154305600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:154302400-154306000	Strong transcription	NHLF	lung
11	chr1:154302400-154306400	Weak transcription	Liver	Liver
12	chr1:154302400-154306400	Strong transcription	NHDF-Ad	bronchial
13	chr1:154302400-154322400	Strong transcription	Dnd41	blood
14	chr1:154302400-154323200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:154302600-154306200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:154302600-154306200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:154302600-154306400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:154302600-154306400	Strong transcription	Stomach Smooth Muscle	stomach
19	chr1:154302600-154306600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:154302600-154307000	Strong transcription	Fetal Stomach	stomach
21	chr1:154302600-154309800	Weak transcription	Fetal Brain Male	brain
22	chr1:154302600-154314400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:154302600-154318200	Weak transcription	Fetal Heart	heart
24	chr1:154302600-154320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:154302600-154322600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:154302600-154323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:154302800-154305800	Strong transcription	Placenta	Placenta
28	chr1:154302800-154306600	Strong transcription	Osteobl	bone
29	chr1:154302800-154307600	Strong transcription	Aorta	Aorta
30	chr1:154302800-154307800	Strong transcription	Brain Germinal Matrix	brain
31	chr1:154302800-154323000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:154303000-154305600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:154303000-154306400	Strong transcription	Brain Substantia Nigra	brain
34	chr1:154303000-154306600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:154303000-154306800	Strong transcription	Brain Anterior Caudate	brain
36	chr1:154303000-154306800	Strong transcription	Brain Hippocampus Middle	brain
37	chr1:154303000-154313000	Weak transcription	Colonic Mucosa	Colon
38	chr1:154303000-154322200	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:154303000-154322600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:154303200-154305600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:154303200-154305600	Strong transcription	HSMMtube	muscle
42	chr1:154303200-154305800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:154303200-154306600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:154303200-154306600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr1:154303200-154306600	Strong transcription	Fetal Muscle Leg	muscle
46	chr1:154303200-154307000	Strong transcription	Spleen	Spleen
47	chr1:154303200-154312800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:154303200-154322200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:154303200-154322400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:154303200-154323400	Strong transcription	Fetal Brain Female	brain

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