Variant report

Variant	rs3845388
Chromosome Location	chr1:179882095-179882096
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	chr1:179864635..179867471-chr1:179879505..179882177,2	K562	blood:
2	chr1:179849629..179853338-chr1:179880600..179883588,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143337	Chromatin interaction
ENSG00000272906	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1048418	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10494523	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10913893	1.00[CHB][hapmap]
rs10913894	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10913895	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10913905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913909	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11590974	1.00[CHB][hapmap]
rs12119431	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12121694	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12126625	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12126967	1.00[CHD][hapmap]
rs12131200	1.00[CHD][hapmap]
rs12136091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141134	1.00[CHD][hapmap]
rs12142457	1.00[CHB][hapmap]
rs12143942	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144346	1.00[CHD][hapmap]
rs12144352	1.00[CHD][hapmap]
rs12144991	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723969	1.00[CHB][hapmap]
rs12756362	1.00[CHB][hapmap]
rs16854910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370139	1.00[CHB][hapmap]
rs17371159	1.00[CHD][hapmap]
rs17371308	1.00[CHD][hapmap]
rs4301600	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61740391	0.92[EUR][1000 genomes]
rs6425596	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6659939	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6673144	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72708661	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72708662	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518566	1.00[CHB][hapmap]
rs7527215	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7531195	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7545581	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7549317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9726605	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
2	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
6	chr1:179854000-179886800	Weak transcription	Fetal Heart	heart
7	chr1:179857600-179886800	Weak transcription	Psoas Muscle	Psoas
8	chr1:179860200-179890200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:179861200-179886600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:179861400-179882200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:179861600-179886600	Weak transcription	Pancreas	Pancrea
12	chr1:179867200-179886600	Weak transcription	Small Intestine	intestine
13	chr1:179867400-179897200	Weak transcription	Stomach Mucosa	stomach
14	chr1:179868200-179891600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr1:179868200-179891800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr1:179868400-179888800	Strong transcription	Adipose Nuclei	Adipose
17	chr1:179868400-179890600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:179868400-179890800	Strong transcription	Dnd41	blood
19	chr1:179868600-179891600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr1:179868600-179892000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:179868800-179889000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:179868800-179889200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:179868800-179889600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:179869000-179888200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:179869200-179885600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:179869200-179891600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:179869400-179889600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:179869400-179891400	Strong transcription	Liver	Liver
29	chr1:179870000-179890400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:179871200-179891000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:179872000-179886600	Weak transcription	Brain Angular Gyrus	brain
32	chr1:179873200-179882600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:179873400-179884600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:179873400-179891400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:179873600-179886400	Weak transcription	HepG2	liver
36	chr1:179874000-179886600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:179874200-179886600	Weak transcription	Fetal Brain Female	brain
38	chr1:179874400-179886800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:179874600-179886000	Weak transcription	Thymus	Thymus
40	chr1:179875200-179891800	Strong transcription	Primary B cells from cord blood	blood
41	chr1:179875600-179882600	Weak transcription	A549	lung
42	chr1:179876000-179891200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:179876800-179883600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:179877000-179888600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:179877000-179891600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:179877200-179888800	Strong transcription	Placenta	Placenta
47	chr1:179877200-179889200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:179877800-179886800	Weak transcription	NHLF	lung
49	chr1:179878000-179882400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:179878000-179886800	Weak transcription	Fetal Kidney	kidney

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