Variant report

Variant	rs35689307
Chromosome Location	chr3:56605512-56605513
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs13060656	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068670	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072654	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074639	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080003	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086565	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088166	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089169	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13089332	0.86[EUR][1000 genomes]
rs13090343	0.89[ASN][1000 genomes]
rs13095165	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825529	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1826119	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34097767	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34171578	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34284682	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34349699	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34480364	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34720351	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869541	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34885435	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34911835	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953718	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35070694	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35286628	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35418695	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35564119	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35677810	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35728519	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35785755	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35803417	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35940731	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35995233	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36029237	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36064180	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36131262	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732506	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4060982	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4538344	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635676	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6807338	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71309961	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71309962	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71309963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71309964	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71309965	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71309970	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71309972	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71309973	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71309975	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71621834	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431634	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv3338042	chr3:56602712-56606910	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3404626	chr3:56603737-56606285	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv3347713	chr3:56604012-56605960	Strong transcription Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
4	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
6	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
7	chr3:56592800-56610200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
9	chr3:56593000-56607800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:56593000-56610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:56593200-56608000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:56593200-56609000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:56593200-56609600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:56593200-56616400	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:56593400-56607600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:56593400-56608600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:56593600-56609800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr3:56594200-56608000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:56594200-56610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:56594400-56609400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:56594800-56609000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:56596000-56605800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr3:56596000-56608400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:56597200-56609200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:56597400-56609400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:56597400-56610000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:56597600-56608000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:56597800-56607600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:56598000-56607000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:56598000-56607800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:56598000-56609200	Strong transcription	Fetal Thymus	thymus
32	chr3:56598000-56609800	Strong transcription	Primary T cells from cord blood	blood
33	chr3:56598600-56608400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:56598600-56609600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:56598800-56607600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:56599600-56606000	Strong transcription	Thymus	Thymus
37	chr3:56599600-56606200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:56599800-56606000	Strong transcription	Fetal Stomach	stomach
39	chr3:56599800-56606200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:56599800-56607800	Strong transcription	Fetal Lung	lung
41	chr3:56599800-56608000	Strong transcription	Liver	Liver
42	chr3:56600000-56606000	Strong transcription	Fetal Intestine Small	intestine
43	chr3:56600000-56606600	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:56600000-56606800	Strong transcription	Osteobl	bone
45	chr3:56600000-56607800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:56600000-56607800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr3:56600000-56607800	Strong transcription	Fetal Muscle Leg	muscle
48	chr3:56600000-56607800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:56600000-56608000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr3:56600000-56608200	Strong transcription	Stomach Smooth Muscle	stomach

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