Variant report

Variant	rs1560411
Chromosome Location	chr3:141596990-141596991
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:141455674..141460093-chr3:141592801..141597430,19	MCF-7	breast:
2	chr3:141455466..141460652-chr3:141593125..141598625,15	K562	blood:
3	chr3:141594674..141598943-chr3:141621711..141625603,5	MCF-7	breast:
4	chr3:141592835..141597303-chr3:141629979..141635181,8	MCF-7	breast:
5	chr3:141455463..141459614-chr3:141593520..141599146,20	K562	blood:
6	chr3:141594460..141597483-chr3:141621419..141624479,3	K562	blood:
7	chr3:141593925..141596999-chr3:141621116..141624479,3	K562	blood:
8	chr3:141452499..141459593-chr3:141591792..141599045,17	MCF-7	breast:
9	chr3:141574992..141577884-chr3:141596784..141598377,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000069849	Chromatin interaction
ENSG00000200389	Chromatin interaction
ENSG00000114125	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10755098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935439	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935440	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935441	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11539489	0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11706195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11707427	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710245	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11721024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11844	0.81[ASN][1000 genomes]
rs12486398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487983	0.81[ASN][1000 genomes]
rs12490893	0.81[ASN][1000 genomes]
rs12497443	0.81[ASN][1000 genomes]
rs16851892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2115935	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288634	0.84[ASN][1000 genomes]
rs2288635	0.84[ASN][1000 genomes]
rs2288636	0.84[ASN][1000 genomes]
rs2861382	0.96[ASN][1000 genomes]
rs36038301	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792410	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3792411	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3804772	0.84[ASN][1000 genomes]
rs3804773	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3828398	0.84[ASN][1000 genomes]
rs4683638	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683640	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683643	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683644	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683646	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683647	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4683649	0.81[ASN][1000 genomes]
rs55945175	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59122181	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7616903	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	esv3333253	chr3:141585303-141602936	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
4	esv3325354	chr3:141594487-141597235	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1560411	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141593400-141597400	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr3:141593400-141597600	Active TSS	Fetal Kidney	kidney
3	chr3:141593400-141597600	Active TSS	HMEC	breast
4	chr3:141593400-141597600	Active TSS	NHLF	lung
5	chr3:141593400-141598000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:141593600-141597000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr3:141593600-141597000	Active TSS	Placenta	Placenta
8	chr3:141593600-141597200	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr3:141593600-141597600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:141593600-141598400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:141593800-141597200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:141593800-141597200	Active TSS	Brain Cingulate Gyrus	brain
13	chr3:141593800-141597200	Active TSS	NH-A	brain
14	chr3:141593800-141597200	Active TSS	NHDF-Ad	bronchial
15	chr3:141593800-141597400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr3:141593800-141597400	Active TSS	Stomach Smooth Muscle	stomach
17	chr3:141593800-141597400	Active TSS	HSMMtube	muscle
18	chr3:141593800-141597600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:141593800-141597600	Active TSS	H9 Cell Line	embryonic stem cell
20	chr3:141593800-141597600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:141593800-141597600	Active TSS	Fetal Intestine Large	intestine
22	chr3:141593800-141597600	Active TSS	HSMM	muscle
23	chr3:141593800-141598000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:141593800-141598000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:141593800-141598000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:141593800-141598400	Active TSS	H1 Cell Line	embryonic stem cell
27	chr3:141594000-141597600	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr3:141594000-141597600	Active TSS	Fetal Muscle Leg	muscle
29	chr3:141594000-141597600	Active TSS	Right Ventricle	heart
30	chr3:141594000-141598000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr3:141594200-141597000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:141594200-141597600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:141594200-141598000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:141594200-141598000	Active TSS	Colonic Mucosa	Colon
35	chr3:141594400-141597000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:141594400-141597000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:141594400-141597000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:141594400-141597000	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr3:141594400-141597000	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr3:141594400-141597000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:141594400-141597000	Active TSS	Ovary	ovary
42	chr3:141594400-141597200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:141594400-141597200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:141594400-141597200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:141594400-141597200	Active TSS	Fetal Muscle Trunk	muscle
46	chr3:141594400-141597200	Active TSS	A549	lung
47	chr3:141594400-141597400	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr3:141594400-141597400	Active TSS	Muscle Satellite Cultured Cells	--
49	chr3:141594400-141597600	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr3:141594400-141597600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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