Variant report

Variant	rs9394282
Chromosome Location	chr6:35188925-35188926
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:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:35186126..35189088-chr6:35223923..35225540,2	K562	blood:
2	chr6:35177824..35181731-chr6:35185438..35190079,5	K562	blood:
3	chr6:35188260..35190147-chr6:35205667..35207207,2	K562	blood:
4	chr6:35086962..35089707-chr6:35186817..35189390,2	K562	blood:
5	chr6:35182167..35187066-chr6:35187567..35191599,8	K562	blood:
6	chr6:35172567..35174119-chr6:35186872..35189196,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCP11-2	chr6:35188147-35189134	NONHSAT112168
2	lnc-TCP11-2	chr6:35188147-35192407	ENSG00000272374.1

No data

Variant related genes	Relation type
ENSG00000146197	Chromatin interaction
ENSG00000124678	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11552398	1.00[GIH][hapmap];0.82[YRI][hapmap]
rs13207848	1.00[GIH][hapmap]
rs13216424	0.88[GIH][hapmap]
rs16871749	1.00[GIH][hapmap]
rs16871814	1.00[GIH][hapmap]
rs1929846	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929848	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234044	1.00[GIH][hapmap]
rs2395617	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756856	1.00[GIH][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap]
rs4713842	1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs4713843	1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs4713844	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713846	0.81[EUR][1000 genomes]
rs6457815	1.00[CHB][hapmap]
rs6906666	1.00[GIH][hapmap]
rs6919534	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931442	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707969	0.82[MEX][hapmap]
rs729925	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734538	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763155	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763157	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751726	1.00[CHB][hapmap]
rs7767150	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770619	1.00[CHB][hapmap]
rs820062	0.88[GIH][hapmap]
rs820065	0.88[GIH][hapmap]
rs820069	0.88[GIH][hapmap]
rs820095	1.00[GIH][hapmap]
rs820099	0.88[GIH][hapmap]
rs820101	0.88[GIH][hapmap]
rs9462081	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9658077	1.00[CHB][hapmap]
rs9658081	1.00[CHB][hapmap]
rs9658085	1.00[CHB][hapmap]
rs9658089	1.00[CHD][hapmap]
rs9658118	1.00[CHD][hapmap]
rs9658119	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9658136	1.00[CHD][hapmap]
rs9658151	1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3428128	chr6:35150524-35225843	Bivalent Enhancer Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9394282	TCP11	cis	lymphoblastoid	seeQTL
rs9394282	TPM2	trans	lymphoblastoid	seeQTL
rs9394282	DEF6	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35182400-35209000	Weak transcription	A549	lung
2	chr6:35182600-35198600	Weak transcription	Gastric	stomach
3	chr6:35183200-35198800	Weak transcription	Ovary	ovary
4	chr6:35183600-35189000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:35184800-35205600	Weak transcription	Fetal Brain Female	brain
6	chr6:35185400-35198800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:35185600-35189200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:35185600-35194200	Enhancers	Fetal Heart	heart
9	chr6:35185800-35198400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:35186200-35202800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:35186400-35198000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:35186400-35212000	Weak transcription	NHDF-Ad	bronchial
13	chr6:35186600-35189600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:35186600-35193200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:35186600-35198200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:35186600-35204600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:35186600-35205400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:35186800-35212000	Weak transcription	Dnd41	blood
19	chr6:35187000-35196400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:35187000-35197600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:35187200-35189800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:35187400-35198400	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:35187600-35198400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:35187800-35192600	Weak transcription	Brain Anterior Caudate	brain
25	chr6:35188000-35190200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:35188000-35191400	Weak transcription	Fetal Stomach	stomach
27	chr6:35188000-35195200	Weak transcription	Lung	lung
28	chr6:35188000-35198400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:35188000-35198600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:35188000-35199400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:35188200-35190000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:35188200-35200400	Genic enhancers	Osteobl	bone
33	chr6:35188200-35205800	Weak transcription	Fetal Kidney	kidney
34	chr6:35188200-35206400	Weak transcription	NH-A	brain
35	chr6:35188400-35189000	Enhancers	HSMMtube	muscle
36	chr6:35188400-35197200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:35188400-35199600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:35188600-35189600	Weak transcription	Right Ventricle	heart
39	chr6:35188600-35195400	Weak transcription	Aorta	Aorta
40	chr6:35188800-35191800	Enhancers	Left Ventricle	heart
41	chr6:35188800-35194600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:35188800-35195200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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