Variant report

Variant	rs4683412
Chromosome Location	chr3:141652242-141652243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141651453..141653933-chr3:141655260..141657163,2	K562	blood:
2	chr3:141645508..141649980-chr3:141650119..141655905,6	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10935439	0.83[AFR][1000 genomes]
rs10935440	0.83[AFR][1000 genomes]
rs10935441	0.83[AFR][1000 genomes]
rs10935445	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10935446	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935447	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11569259	0.88[EUR][1000 genomes]
rs11569262	0.88[EUR][1000 genomes]
rs11569278	0.88[EUR][1000 genomes]
rs11569281	0.91[EUR][1000 genomes]
rs11569291	0.91[EUR][1000 genomes]
rs11707100	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11707427	0.83[AFR][1000 genomes]
rs11711748	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11713023	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11844	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12487977	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12487983	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12490893	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12494971	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12497112	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12497443	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1808584	0.93[ASN][1000 genomes]
rs2288634	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2288635	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2288636	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34071952	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3762726	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3804772	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3828398	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4683413	0.88[EUR][1000 genomes]
rs4683414	0.88[EUR][1000 genomes]
rs4683638	0.83[AFR][1000 genomes]
rs4683649	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683651	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4683652	0.93[EUR][1000 genomes]
rs56174413	0.90[ASN][1000 genomes]
rs59122181	0.83[AFR][1000 genomes]
rs745966	1.00[AFR][1000 genomes];1.00[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	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
rs4683412	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141621000-141670800	Weak transcription	Small Intestine	intestine
2	chr3:141623600-141652400	Strong transcription	Fetal Thymus	thymus
3	chr3:141625600-141668400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:141626600-141659000	Weak transcription	Pancreas	Pancrea
5	chr3:141627800-141652600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:141628200-141673600	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:141628600-141658800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:141628600-141669000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:141628800-141669800	Weak transcription	Fetal Lung	lung
10	chr3:141628800-141674000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
12	chr3:141632400-141654000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:141633000-141659000	Weak transcription	NHLF	lung
14	chr3:141634200-141682000	Weak transcription	Brain Angular Gyrus	brain
15	chr3:141634400-141656600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:141635800-141652400	Weak transcription	HSMM	muscle
17	chr3:141635800-141652600	Strong transcription	Thymus	Thymus
18	chr3:141637400-141658800	Weak transcription	Brain Germinal Matrix	brain
19	chr3:141640600-141656400	Weak transcription	Fetal Brain Male	brain
20	chr3:141640600-141658800	Weak transcription	Fetal Heart	heart
21	chr3:141640800-141659200	Weak transcription	Colonic Mucosa	Colon
22	chr3:141640800-141659200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:141641000-141652800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:141642800-141658600	Weak transcription	A549	lung
25	chr3:141643000-141656400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:141643000-141656400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:141643000-141675800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:141643400-141671200	Weak transcription	Right Ventricle	heart
29	chr3:141644800-141652400	Weak transcription	HSMMtube	muscle
30	chr3:141644800-141658600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:141644800-141658600	Weak transcription	NHDF-Ad	bronchial
32	chr3:141644800-141678400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:141645400-141653000	Strong transcription	Fetal Intestine Small	intestine
34	chr3:141646800-141656400	Weak transcription	K562	blood
35	chr3:141646800-141659000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:141646800-141668200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:141647000-141656200	Weak transcription	HMEC	breast
38	chr3:141647000-141656400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:141647000-141656400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:141647000-141668400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:141647000-141669200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:141647200-141652600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:141647200-141656400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:141647200-141656400	Weak transcription	NHEK	skin
45	chr3:141647200-141656600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:141647200-141658800	Weak transcription	NH-A	brain
47	chr3:141647200-141659000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:141647200-141669400	Weak transcription	Primary B cells from cord blood	blood
49	chr3:141647400-141652800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:141647400-141656400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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