Variant report

Variant	rs1572058
Chromosome Location	chr1:57041537-57041538
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11206845	0.81[AFR][1000 genomes]
rs11206846	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.91[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	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11810635	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058536	0.81[AFR][1000 genomes]
rs12059747	0.90[ASW][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs12059843	0.81[AFR][1000 genomes]
rs12070247	0.90[ASW][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs12070557	0.81[AFR][1000 genomes]
rs12090895	0.81[AFR][1000 genomes]
rs12098117	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs1418521	1.00[CEU][hapmap];0.81[MKK][hapmap];0.90[YRI][hapmap]
rs17114100	1.00[CEU][hapmap]
rs17114110	1.00[CEU][hapmap]
rs17114113	1.00[CEU][hapmap]
rs17114115	1.00[CEU][hapmap]
rs17114126	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs17114127	1.00[CEU][hapmap]
rs28673510	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41446844	0.90[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56332336	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661359	0.81[AFR][1000 genomes];0.91[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	0.81[AFR][1000 genomes]
rs72664373	0.96[ASN][1000 genomes]
rs72664400	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72903425	0.81[AFR][1000 genomes]
rs7539051	1.00[ASW][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[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:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57029400-57042200	Weak transcription	Thymus	Thymus
2	chr1:57032400-57042400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:57036800-57041600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:57037200-57042400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:57037200-57042400	Weak transcription	Gastric	stomach
6	chr1:57038000-57043400	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr1:57038000-57043800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:57038200-57042400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:57038200-57042400	Weak transcription	Esophagus	oesophagus
10	chr1:57038400-57043200	Weak transcription	Spleen	Spleen
11	chr1:57039000-57042000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:57039000-57042400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:57039000-57042600	Active TSS	Psoas Muscle	Psoas
14	chr1:57039200-57041600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:57039200-57042400	Active TSS	Stomach Smooth Muscle	stomach
16	chr1:57039400-57041600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:57039400-57042400	Weak transcription	Hela-S3	cervix
18	chr1:57039600-57042000	Weak transcription	Fetal Intestine Large	intestine
19	chr1:57039600-57042200	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:57039600-57042200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr1:57039600-57042200	Weak transcription	Fetal Heart	heart
22	chr1:57039600-57042400	Active TSS	Rectal Smooth Muscle	rectum
23	chr1:57039600-57043200	Active TSS	NHLF	lung
24	chr1:57039600-57046000	Active TSS	Right Atrium	heart
25	chr1:57040000-57042400	Active TSS	Fetal Kidney	kidney
26	chr1:57040000-57042600	Active TSS	Fetal Brain Female	brain
27	chr1:57040000-57042600	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr1:57040000-57042800	Enhancers	Primary B cells from peripheral blood	blood
29	chr1:57040000-57045600	Active TSS	Brain Angular Gyrus	brain
30	chr1:57040000-57046000	Active TSS	Ovary	ovary
31	chr1:57040200-57042400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:57040200-57042400	Weak transcription	Lung	lung
33	chr1:57040200-57042800	Enhancers	Primary B cells from cord blood	blood
34	chr1:57040200-57042800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:57040200-57042800	Active TSS	Fetal Muscle Leg	muscle
36	chr1:57040200-57043400	Active TSS	Placenta	Placenta
37	chr1:57040200-57043600	Active TSS	Fetal Muscle Trunk	muscle
38	chr1:57040200-57043800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:57040200-57044200	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr1:57040200-57045800	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr1:57040200-57046000	Active TSS	Right Ventricle	heart
42	chr1:57040400-57041600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr1:57040400-57041600	Active TSS	Brain Germinal Matrix	brain
44	chr1:57040400-57041800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
45	chr1:57040400-57042400	Weak transcription	Small Intestine	intestine
46	chr1:57040400-57045600	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr1:57040600-57041600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:57040600-57041600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr1:57040600-57041600	Active TSS	HSMM	muscle
50	chr1:57040600-57042000	Enhancers	Fetal Intestine Small	intestine

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