Variant report

Variant	rs56332336
Chromosome Location	chr1:57034790-57034791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:57007850..57009475-chr1:57034148..57036115,2	MCF-7	breast:
2	chr1:57034051..57037170-chr1:57042979..57045749,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162407	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10888981	0.81[AFR][1000 genomes]
rs11206845	0.97[AFR][1000 genomes]
rs11206846	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800865	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11800883	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11810635	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058536	0.97[AFR][1000 genomes]
rs12059747	0.97[AFR][1000 genomes]
rs12059843	0.97[AFR][1000 genomes]
rs12070247	0.97[AFR][1000 genomes]
rs12070557	0.97[AFR][1000 genomes]
rs12090895	0.97[AFR][1000 genomes]
rs12098117	0.97[AFR][1000 genomes]
rs1572058	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673510	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41446844	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661359	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699960	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6702052	0.97[AFR][1000 genomes]
rs72664373	0.96[ASN][1000 genomes]
rs72664400	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72903425	0.97[AFR][1000 genomes]
rs7539051	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57016000-57038600	Weak transcription	HSMMtube	muscle
2	chr1:57017400-57035400	Weak transcription	Esophagus	oesophagus
3	chr1:57017400-57035400	Weak transcription	Fetal Thymus	thymus
4	chr1:57017400-57039400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:57017800-57040800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:57025600-57040000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:57028000-57035400	Weak transcription	Colonic Mucosa	Colon
8	chr1:57028800-57035400	Weak transcription	Gastric	stomach
9	chr1:57029400-57042200	Weak transcription	Thymus	Thymus
10	chr1:57030000-57035400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:57030800-57036800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:57031000-57035400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr1:57032000-57035400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:57032000-57035400	Weak transcription	Spleen	Spleen
15	chr1:57032000-57035400	Genic enhancers	NHDF-Ad	bronchial
16	chr1:57032000-57035600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:57032000-57036800	Weak transcription	Fetal Stomach	stomach
18	chr1:57032000-57038800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:57032200-57035400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:57032200-57035400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:57032200-57035400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:57032200-57035400	Weak transcription	Ovary	ovary
23	chr1:57032200-57035400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:57032200-57035400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:57032200-57035400	Weak transcription	Stomach Mucosa	stomach
26	chr1:57032200-57038000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:57032200-57040600	Weak transcription	HSMM	muscle
28	chr1:57032400-57035400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:57032400-57035400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:57032400-57035400	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:57032400-57035400	Weak transcription	Right Ventricle	heart
32	chr1:57032400-57042400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:57032600-57035200	Weak transcription	A549	lung
34	chr1:57032600-57035600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:57032600-57035600	Weak transcription	Adipose Nuclei	Adipose
36	chr1:57032600-57036800	Weak transcription	Fetal Heart	heart
37	chr1:57032800-57035200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:57032800-57035200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:57032800-57035200	Enhancers	HepG2	liver
40	chr1:57032800-57035400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:57032800-57035400	Weak transcription	Brain Germinal Matrix	brain
42	chr1:57032800-57036600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr1:57032800-57037600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:57032800-57038200	Weak transcription	Osteobl	bone
45	chr1:57032800-57039200	Weak transcription	Small Intestine	intestine
46	chr1:57032800-57041000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:57033000-57035200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:57033000-57035200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:57033000-57035400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr1:57033000-57035400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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