Variant report

Variant	rs4683646
Chromosome Location	chr3:141625115-141625116
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	chr3:141594674..141598943-chr3:141621711..141625603,5	MCF-7	breast:
2	chr3:141622629..141625645-chr3:141628470..141632176,3	K562	blood:

Variant related genes	Relation type
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10755098	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935439	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935440	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935441	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935442	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935443	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11539489	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11706195	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11707427	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721024	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11844	0.86[ASN][1000 genomes]
rs12486398	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487977	0.84[ASN][1000 genomes]
rs12487983	0.86[ASN][1000 genomes]
rs12490893	0.86[ASN][1000 genomes]
rs12497443	0.86[ASN][1000 genomes]
rs1560411	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16851892	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2115935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288634	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2288635	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2288636	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2861382	0.96[ASN][1000 genomes]
rs34071952	0.84[ASN][1000 genomes]
rs36038301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792410	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804772	0.89[ASN][1000 genomes]
rs3804773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828398	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4683638	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683639	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683640	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683641	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683642	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683647	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4683649	0.86[ASN][1000 genomes]
rs4683651	0.83[ASN][1000 genomes]
rs55945175	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59122181	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7616903	0.97[EUR][1000 genomes];0.97[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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4683646	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141596400-141626400	Weak transcription	Pancreas	Pancrea
2	chr3:141597000-141625200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:141597200-141625800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:141597800-141627000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:141598000-141625400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:141598000-141626000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:141598000-141627000	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:141598000-141627200	Weak transcription	Colonic Mucosa	Colon
10	chr3:141598000-141642000	Weak transcription	Right Ventricle	heart
11	chr3:141598200-141626000	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:141598200-141627200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:141598200-141640200	Weak transcription	Fetal Brain Male	brain
14	chr3:141598200-141640200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:141605200-141627200	Weak transcription	Primary T cells from cord blood	blood
16	chr3:141606800-141625200	Weak transcription	HSMMtube	muscle
17	chr3:141614000-141626000	Weak transcription	Fetal Lung	lung
18	chr3:141614800-141625200	Weak transcription	NHDF-Ad	bronchial
19	chr3:141616200-141625800	Weak transcription	NHLF	lung
20	chr3:141616200-141627000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:141616200-141646600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:141616200-141648600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:141616400-141626000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:141616800-141627200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:141618000-141633600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr3:141619200-141625800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:141619400-141625200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:141619400-141625200	Weak transcription	Adipose Nuclei	Adipose
29	chr3:141619400-141625400	Weak transcription	Primary B cells from cord blood	blood
30	chr3:141619400-141625400	Weak transcription	Fetal Brain Female	brain
31	chr3:141619400-141626400	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:141619400-141627200	Weak transcription	Brain Germinal Matrix	brain
33	chr3:141619400-141641600	Weak transcription	Ovary	ovary
34	chr3:141619600-141625200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:141619600-141625200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:141619600-141625200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:141619600-141625200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:141619600-141625600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:141619600-141625800	Weak transcription	Lung	lung
40	chr3:141619600-141626000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:141619600-141626000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:141619600-141626000	Weak transcription	Thymus	Thymus
43	chr3:141619600-141627000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:141619600-141628400	Weak transcription	Psoas Muscle	Psoas
45	chr3:141619600-141640200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:141619600-141644000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:141619800-141625200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:141619800-141626200	Weak transcription	Fetal Stomach	stomach
49	chr3:141619800-141633200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:141620400-141641200	Weak transcription	Spleen	Spleen

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