Variant report

Variant	rs9394167
Chromosome Location	chr6:33754396-33754397
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	chr6:33753782-33754414	HepG2	liver:	n/a	n/a
2	CHD1	chr6:33753489-33757327	IMR90	lung:	n/a	n/a
3	POLR2A	chr6:33754307-33756475	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr6:33753458-33754807	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr6:33754123-33757999	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr6:33754388-33756268	K562	blood:	n/a	n/a
7	POLR2A	chr6:33753986-33754634	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33677771..33685795-chr6:33753004..33758704,10	MCF-7	breast:
2	chr6:33743776..33747465-chr6:33751783..33755243,5	MCF-7	breast:
3	chr6:33752857..33754428-chr6:33763521..33765942,2	MCF-7	breast:

Variant related genes	Relation type
LEMD2	TF binding region
ENSG00000137288	Chromatin interaction
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12173787	0.89[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12190029	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2013365	0.90[AFR][1000 genomes]
rs2281820	0.80[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs2296744	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2296746	0.81[AFR][1000 genomes]
rs2296747	0.93[AFR][1000 genomes]
rs2296748	0.89[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs2395402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711347	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4711348	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4711349	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713678	0.81[EUR][1000 genomes]
rs4713679	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713681	0.93[AFR][1000 genomes]
rs6457741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6929696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747694	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs751728	0.88[AFR][1000 genomes]
rs7774620	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9357164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380378	0.89[AFR][1000 genomes]
rs9394166	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs943471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs943474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943475	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv3436027	chr6:33754374-33758772	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9394167	PSMB9	cis	lymphoblastoid	seeQTL
rs9394167	LEMD2	cis	parietal	SCAN
rs9394167	LEMD2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33744200-33754400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:33746600-33755000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:33750400-33755000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:33751600-33754400	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr6:33751600-33755200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:33751800-33754600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:33752000-33754400	Genic enhancers	Left Ventricle	heart
8	chr6:33752000-33754600	Genic enhancers	Adipose Nuclei	Adipose
9	chr6:33752000-33754600	Weak transcription	Fetal Brain Male	brain
10	chr6:33752000-33755000	Genic enhancers	Brain Cingulate Gyrus	brain
11	chr6:33752400-33754400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr6:33752400-33754400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr6:33752400-33754400	Genic enhancers	Pancreas	Pancrea
14	chr6:33752400-33754400	Genic enhancers	Rectal Smooth Muscle	rectum
15	chr6:33752400-33754600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr6:33752400-33754800	Genic enhancers	Stomach Smooth Muscle	stomach
17	chr6:33752600-33754400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:33752600-33754400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:33752600-33754400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:33752600-33754600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
21	chr6:33752600-33754600	Genic enhancers	Colon Smooth Muscle	Colon
22	chr6:33752600-33755000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:33752600-33755200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:33752600-33755600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:33752800-33754400	Genic enhancers	Muscle Satellite Cultured Cells	--
26	chr6:33752800-33754800	Genic enhancers	Osteobl	bone
27	chr6:33752800-33755200	Genic enhancers	Brain Hippocampus Middle	brain
28	chr6:33752800-33755400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:33752800-33755400	Genic enhancers	Fetal Muscle Leg	muscle
30	chr6:33752800-33755400	Genic enhancers	Placenta	Placenta
31	chr6:33753000-33754400	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr6:33753000-33754400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr6:33753000-33754400	Genic enhancers	Lung	lung
34	chr6:33753000-33754400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr6:33753000-33754400	Genic enhancers	Rectal Mucosa Donor 29	rectum
36	chr6:33753000-33754400	Genic enhancers	HMEC	breast
37	chr6:33753000-33754600	Genic enhancers	Primary T cells from cord blood	blood
38	chr6:33753000-33754600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:33753000-33754600	Genic enhancers	Liver	Liver
40	chr6:33753000-33754800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:33753000-33754800	Genic enhancers	Brain Substantia Nigra	brain
42	chr6:33753000-33754800	Genic enhancers	Fetal Lung	lung
43	chr6:33753000-33755200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:33753000-33755200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:33753000-33755200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:33753000-33755200	Genic enhancers	HSMM	muscle
47	chr6:33753000-33755400	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr6:33753000-33756000	Flanking Active TSS	HUVEC	blood vessel
49	chr6:33753200-33754400	Genic enhancers	Primary hematopoietic stem cells	blood
50	chr6:33753200-33754600	Weak transcription	Aorta	Aorta

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