Variant report

Variant	rs59509062
Chromosome Location	chr3:100117163-100117164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100052074..100055881-chr3:100116822..100121530,5	MCF-7	breast:
2	chr3:100064881..100067551-chr3:100115923..100118439,2	MCF-7	breast:
3	chr3:100097916..100106101-chr3:100115627..100122137,10	K562	blood:
4	chr3:100116980..100119109-chr3:100147635..100150466,2	K562	blood:
5	chr3:100097916..100101332-chr3:100115627..100118709,3	K562	blood:

Variant related genes	Relation type
ENSG00000154174	Chromatin interaction
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11918399	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11919543	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11919627	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16842142	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3772687	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55699261	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55864663	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56012915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56956506	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57155242	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57166766	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57332305	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57703319	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59304656	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59396265	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59491720	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59507591	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60463428	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60999188	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941434	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72941452	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941453	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941454	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941473	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941482	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873033	0.81[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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 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	chr3:100090200-100118400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:100091600-100117600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:100099000-100118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:100099800-100117600	Weak transcription	Colonic Mucosa	Colon
5	chr3:100102800-100118200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:100103800-100117600	Weak transcription	Fetal Kidney	kidney
7	chr3:100103800-100118600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:100104000-100117600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:100104200-100117600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:100104200-100117600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:100104200-100117600	Weak transcription	Psoas Muscle	Psoas
12	chr3:100104200-100117600	Weak transcription	Thymus	Thymus
13	chr3:100104200-100117800	Weak transcription	Esophagus	oesophagus
14	chr3:100104200-100118200	Weak transcription	HSMMtube	muscle
15	chr3:100104200-100118600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:100104200-100118600	Weak transcription	Aorta	Aorta
17	chr3:100104400-100117200	Weak transcription	NHEK	skin
18	chr3:100104600-100117600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:100104600-100117600	Weak transcription	Fetal Brain Male	brain
20	chr3:100104600-100118600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:100104800-100117400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:100105200-100117600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:100105200-100118400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:100105200-100118600	Weak transcription	Placenta	Placenta
25	chr3:100105800-100118200	Weak transcription	HMEC	breast
26	chr3:100106000-100117600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:100106000-100117800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:100106200-100117400	Weak transcription	Osteobl	bone
29	chr3:100106200-100117800	Weak transcription	NH-A	brain
30	chr3:100106200-100118200	Weak transcription	HUVEC	blood vessel
31	chr3:100106400-100117400	Weak transcription	Fetal Heart	heart
32	chr3:100106400-100117800	Weak transcription	Lung	lung
33	chr3:100106400-100117800	Weak transcription	Ovary	ovary
34	chr3:100106400-100118200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:100106600-100117800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:100108200-100117400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:100108200-100117600	Weak transcription	Fetal Lung	lung
38	chr3:100108400-100118200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:100108400-100118200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:100108600-100118400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:100108800-100117600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:100109200-100117400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:100109200-100117600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:100109200-100117600	Weak transcription	Fetal Brain Female	brain
45	chr3:100109200-100118200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:100109400-100117400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:100109400-100117800	Weak transcription	HSMM	muscle
48	chr3:100109400-100118200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:100109400-100118200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:100109400-100118200	Weak transcription	Monocytes-CD14+_RO01746	blood

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