Variant report

Variant	rs1365550
Chromosome Location	chr4:119771606-119771607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119756043..119758170-chr4:119769333..119772030,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNPO2-1	chr4:119771440-119773194	NONHSAT098023
2	lnc-SYNPO2-1	chr4:119771465-119771743	NONHSAT098024

Variant related genes	Relation type
ENSG00000150961	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1019696	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11098453	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11098459	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098460	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11722846	1.00[YRI][hapmap]
rs11931472	1.00[YRI][hapmap]
rs12512594	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12643205	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13112913	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13139244	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1365549	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1365551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962840	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2114461	0.93[ASN][1000 genomes]
rs2303512	0.82[CEU][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes]
rs2389688	0.87[ASN][1000 genomes]
rs34057511	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35934778	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36096663	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3775839	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3775840	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3885192	0.83[ASN][1000 genomes]
rs4833592	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4833593	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4834704	0.87[AMR][1000 genomes]
rs4834705	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4834706	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6811006	0.91[CEU][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6817084	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7375858	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3376985	chr4:119757182-119774736	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119764800-119771800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:119770600-119772000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr4:119770600-119772000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr4:119770800-119771800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr4:119771000-119772800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr4:119771000-119773400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr4:119771200-119772400	Active TSS	Aorta	Aorta
8	chr4:119771200-119772400	Active TSS	Stomach Smooth Muscle	stomach
9	chr4:119771200-119772800	Flanking Active TSS	Dnd41	blood
10	chr4:119771200-119773400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr4:119771200-119773600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr4:119771400-119771800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr4:119771400-119771800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:119771400-119771800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:119771400-119771800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr4:119771400-119771800	Enhancers	Spleen	Spleen
17	chr4:119771400-119771800	Flanking Active TSS	NHEK	skin
18	chr4:119771400-119771800	Flanking Active TSS	Osteobl	bone
19	chr4:119771400-119772000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:119771400-119772000	Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr4:119771400-119772000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr4:119771400-119772000	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr4:119771400-119772000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:119771400-119772000	Active TSS	Liver	Liver
25	chr4:119771400-119772000	Active TSS	Fetal Kidney	kidney
26	chr4:119771400-119772000	Active TSS	Rectal Smooth Muscle	rectum
27	chr4:119771400-119772200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:119771400-119772200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:119771400-119772200	Active TSS	Brain Anterior Caudate	brain
30	chr4:119771400-119772200	Active TSS	Brain Cingulate Gyrus	brain
31	chr4:119771400-119772200	Active TSS	Brain Hippocampus Middle	brain
32	chr4:119771400-119772200	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr4:119771400-119772200	Active TSS	Brain Substantia Nigra	brain
34	chr4:119771400-119772200	Active TSS	Colonic Mucosa	Colon
35	chr4:119771400-119772200	Active TSS	Colon Smooth Muscle	Colon
36	chr4:119771400-119772200	Active TSS	Duodenum Mucosa	Duodenum
37	chr4:119771400-119772200	Enhancers	Fetal Heart	heart
38	chr4:119771400-119772200	Active TSS	Left Ventricle	heart
39	chr4:119771400-119772200	Active TSS	Right Ventricle	heart
40	chr4:119771400-119772400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:119771400-119772400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:119771400-119772400	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr4:119771400-119772400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr4:119771400-119772400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr4:119771400-119772400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:119771400-119772400	Active TSS	Adipose Nuclei	Adipose
47	chr4:119771400-119772400	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr4:119771400-119772400	Active TSS	Ovary	ovary
49	chr4:119771400-119772400	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr4:119771400-119772400	Active TSS	NHLF	lung

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