Variant report

Variant	rs59304656
Chromosome Location	chr3:100117765-100117766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:100117646-100118083	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

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	chr3:100106736..100109063-chr3:100117268..100119845,2	K562	blood:
4	chr3:100097916..100106101-chr3:100115627..100122137,10	K562	blood:
5	chr3:100093392..100095134-chr3:100117257..100119612,2	K562	blood:
6	chr3:100116980..100119109-chr3:100147635..100150466,2	K562	blood:
7	chr3:99996650..99998446-chr3:100117737..100119944,2	K562	blood:
8	chr3:100099401..100103527-chr3:100117550..100121361,6	MCF-7	breast:
9	chr3:100097916..100101332-chr3:100115627..100118709,3	K562	blood:

No data

Variant related genes	Relation type
LNP1	TF binding region
ENSG00000114021	Chromatin interaction
ENSG00000036054	Chromatin interaction
ENSG00000154174	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	0.81[AFR][1000 genomes];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]
rs59396265	0.91[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	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59509062	0.98[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	0.88[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	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941482	0.98[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:119 , 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	chr3:100099000-100118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:100102800-100118200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:100103800-100118600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:100104200-100117800	Weak transcription	Esophagus	oesophagus
6	chr3:100104200-100118200	Weak transcription	HSMMtube	muscle
7	chr3:100104200-100118600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:100104200-100118600	Weak transcription	Aorta	Aorta
9	chr3:100104600-100118600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:100105200-100118400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:100105200-100118600	Weak transcription	Placenta	Placenta
12	chr3:100105800-100118200	Weak transcription	HMEC	breast
13	chr3:100106000-100117800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:100106200-100117800	Weak transcription	NH-A	brain
15	chr3:100106200-100118200	Weak transcription	HUVEC	blood vessel
16	chr3:100106400-100117800	Weak transcription	Lung	lung
17	chr3:100106400-100117800	Weak transcription	Ovary	ovary
18	chr3:100106400-100118200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:100106600-100117800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:100108400-100118200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:100108400-100118200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:100108600-100118400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:100109200-100118200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:100109400-100117800	Weak transcription	HSMM	muscle
25	chr3:100109400-100118200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:100109400-100118200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:100109400-100118200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr3:100109600-100117800	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:100109600-100118200	Weak transcription	Primary B cells from cord blood	blood
30	chr3:100109800-100118000	Weak transcription	Fetal Thymus	thymus
31	chr3:100109800-100118600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:100110400-100118800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:100112800-100118400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr3:100113200-100118200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:100113400-100117800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:100113400-100118200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:100114400-100117800	Enhancers	Liver	Liver
38	chr3:100114400-100118800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:100114600-100117800	Enhancers	HepG2	liver
40	chr3:100114600-100118200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr3:100114600-100118200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr3:100115000-100118200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:100115000-100118600	Weak transcription	Stomach Mucosa	stomach
44	chr3:100115200-100117800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:100115200-100118200	Weak transcription	Small Intestine	intestine
46	chr3:100116000-100117800	Weak transcription	Fetal Intestine Large	intestine
47	chr3:100116200-100118200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:100116200-100118200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:100116400-100117800	Enhancers	Right Ventricle	heart
50	chr3:100116400-100118400	Enhancers	Fetal Muscle Trunk	muscle

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