Variant report

Variant	rs528761
Chromosome Location	chr6:143821234-143821235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:143820850-143821538	K562	blood:	n/a	n/a
2	POLR2A	chr6:143821153-143821359	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:143818729..143821756-chr6:143830750..143834013,3	MCF-7	breast:
2	chr6:143804689..143809307-chr6:143816988..143822898,5	K562	blood:
3	chr6:143821189..143823852-chr6:143831025..143833660,2	MCF-7	breast:
4	chr6:143760601..143762958-chr6:143820757..143822738,2	K562	blood:

Variant related genes	Relation type
ENSG00000229036	TF binding region
ENSG00000229036	Chromatin interaction
ENSG00000034693	Chromatin interaction
ENSG00000001036	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1116	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs161056	0.87[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs161058	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs161061	0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs161062	0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs161065	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs161066	0.92[ASN][1000 genomes]
rs161068	0.94[ASN][1000 genomes]
rs161069	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs161072	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs161074	0.94[YRI][hapmap];0.92[ASN][1000 genomes]
rs161075	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[ASN][1000 genomes]
rs161076	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs161077	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs170343	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];0.94[EUR][1000 genomes]
rs223228	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs223230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs505481	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs509185	0.94[EUR][1000 genomes]
rs511839	0.94[EUR][1000 genomes]
rs8161	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs9390095	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496646	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	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
rs528761	PEX3	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 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	chr6:143798800-143821400	Weak transcription	HMEC	breast
12	chr6:143799000-143827000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:143800800-143831000	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:143805200-143827800	Weak transcription	Fetal Heart	heart
15	chr6:143811400-143832000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:143811800-143829400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr6:143812000-143827400	Weak transcription	Pancreas	Pancrea
18	chr6:143812200-143831600	Weak transcription	Right Ventricle	heart
19	chr6:143812400-143826800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:143812400-143829600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:143812400-143832200	Weak transcription	Spleen	Spleen
22	chr6:143812600-143831800	Weak transcription	NHEK	skin
23	chr6:143812600-143832000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:143813000-143826600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:143813400-143828400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr6:143813400-143829600	Strong transcription	Fetal Intestine Large	intestine
27	chr6:143813800-143828400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:143814200-143825600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr6:143814200-143828200	Strong transcription	HSMM	muscle
30	chr6:143814200-143828800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:143814200-143829600	Strong transcription	K562	blood
32	chr6:143814400-143825600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:143814400-143830200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr6:143814600-143823800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr6:143814600-143828200	Strong transcription	HepG2	liver
36	chr6:143814600-143828600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:143814600-143831000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:143814800-143822200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:143814800-143825400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:143814800-143825400	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr6:143814800-143827200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:143814800-143828200	Strong transcription	Left Ventricle	heart
43	chr6:143814800-143828200	Strong transcription	NHLF	lung
44	chr6:143814800-143828400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:143814800-143828400	Strong transcription	Adipose Nuclei	Adipose
46	chr6:143814800-143829000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:143814800-143829200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr6:143814800-143829400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:143814800-143831400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:143815000-143821800	Strong transcription	Colonic Mucosa	Colon

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