Variant report

Variant	rs3789791
Chromosome Location	chr6:143823967-143823968
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143810260..143812960-chr6:143821812..143824158,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241847	Chromatin interaction
ENSG00000229036	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1065355	0.87[EUR][1000 genomes]
rs10782288	0.88[EUR][1000 genomes]
rs10782289	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10809	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12196227	0.87[EUR][1000 genomes]
rs12199192	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1338533	0.90[EUR][1000 genomes]
rs1424922	0.86[EUR][1000 genomes]
rs1978529	0.93[EUR][1000 genomes]
rs2143137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294505	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3762000	0.88[EUR][1000 genomes]
rs3762001	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762002	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789789	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3789790	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804538	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804539	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804544	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4895615	0.89[EUR][1000 genomes]
rs4896659	0.87[EUR][1000 genomes]
rs4896660	0.88[EUR][1000 genomes]
rs6924268	0.88[EUR][1000 genomes]
rs6926733	0.86[EUR][1000 genomes]
rs6930325	0.89[EUR][1000 genomes]
rs6935346	0.89[EUR][1000 genomes]
rs6935618	0.86[EUR][1000 genomes]
rs7741976	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7751011	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9321913	0.87[EUR][1000 genomes]
rs9321914	0.88[EUR][1000 genomes]
rs9373393	0.88[EUR][1000 genomes]
rs9376750	0.87[EUR][1000 genomes]
rs9376753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390094	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9390096	0.88[EUR][1000 genomes]
rs9399442	0.86[EUR][1000 genomes]
rs9399443	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9403492	0.87[EUR][1000 genomes]
rs9403494	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9403496	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	esv2757193	chr6:143820009-143825104	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2759475	chr6:143820009-143825104	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3789791	PEX3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143772600-143832000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:143773200-143827000	Weak transcription	Brain Germinal Matrix	brain
3	chr6:143773400-143832000	Weak transcription	Fetal Brain Male	brain
4	chr6:143781000-143832000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:143790200-143831600	Weak transcription	Esophagus	oesophagus
6	chr6:143790200-143831600	Weak transcription	Gastric	stomach
7	chr6:143795200-143827400	Weak transcription	Aorta	Aorta
8	chr6:143795800-143831800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:143797000-143826600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:143797600-143831000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:143799000-143827000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:143800800-143831000	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:143805200-143827800	Weak transcription	Fetal Heart	heart
14	chr6:143811400-143832000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:143811800-143829400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr6:143812000-143827400	Weak transcription	Pancreas	Pancrea
17	chr6:143812200-143831600	Weak transcription	Right Ventricle	heart
18	chr6:143812400-143826800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:143812400-143829600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:143812400-143832200	Weak transcription	Spleen	Spleen
21	chr6:143812600-143831800	Weak transcription	NHEK	skin
22	chr6:143812600-143832000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:143813000-143826600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:143813400-143828400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr6:143813400-143829600	Strong transcription	Fetal Intestine Large	intestine
26	chr6:143813800-143828400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:143814200-143825600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr6:143814200-143828200	Strong transcription	HSMM	muscle
29	chr6:143814200-143828800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:143814200-143829600	Strong transcription	K562	blood
31	chr6:143814400-143825600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:143814400-143830200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr6:143814600-143828200	Strong transcription	HepG2	liver
34	chr6:143814600-143828600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:143814600-143831000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:143814800-143825400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:143814800-143825400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr6:143814800-143827200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:143814800-143828200	Strong transcription	Left Ventricle	heart
40	chr6:143814800-143828200	Strong transcription	NHLF	lung
41	chr6:143814800-143828400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:143814800-143828400	Strong transcription	Adipose Nuclei	Adipose
43	chr6:143814800-143829000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:143814800-143829200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr6:143814800-143829400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:143814800-143831400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:143815000-143826000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:143815000-143828400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:143815000-143829000	Strong transcription	Liver	Liver
50	chr6:143815200-143825600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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