Variant report

Variant	rs4713843
Chromosome Location	chr6:35203745-35203746
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:35195154..35200305-chr6:35202213..35207133,5	K562	blood:
2	chr6:35203567..35205850-chr6:35210606..35213440,2	MCF-7	breast:
3	chr6:35203262..35205063-chr6:35205452..35207429,2	K562	blood:
4	chr6:35132585..35134492-chr6:35202340..35203841,2	MCF-7	breast:
5	chr6:35196327..35198090-chr6:35203601..35206096,2	MCF-7	breast:
6	chr6:34938891..34940598-chr6:35202108..35204116,2	K562	blood:
7	chr6:35196232..35199243-chr6:35200230..35204307,5	K562	blood:
8	chr6:35202209..35206634-chr6:35208195..35211678,7	K562	blood:

No data

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11962571	0.88[YRI][hapmap]
rs1929848	0.82[MEX][hapmap]
rs2395617	0.80[EUR][1000 genomes]
rs4713842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713846	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs4713854	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs6913026	0.88[YRI][hapmap]
rs6919534	0.82[MEX][hapmap]
rs6931442	0.81[EUR][1000 genomes]
rs6937483	0.88[YRI][hapmap]
rs707969	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs729925	1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs734538	1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs763155	1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs763157	1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs7754530	0.88[YRI][hapmap]
rs7757196	1.00[YRI][hapmap]
rs7767150	0.83[EUR][1000 genomes]
rs9394282	1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs9658056	0.88[YRI][hapmap]
rs9658136	1.00[YRI][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4713843	DEF6	cis	multi-tissue	Pritchard
rs4713843	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35182400-35209000	Weak transcription	A549	lung
2	chr6:35184800-35205600	Weak transcription	Fetal Brain Female	brain
3	chr6:35186400-35212000	Weak transcription	NHDF-Ad	bronchial
4	chr6:35186600-35204600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:35186600-35205400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:35186800-35212000	Weak transcription	Dnd41	blood
7	chr6:35188200-35205800	Weak transcription	Fetal Kidney	kidney
8	chr6:35188200-35206400	Weak transcription	NH-A	brain
9	chr6:35189600-35205800	Weak transcription	Brain Germinal Matrix	brain
10	chr6:35190000-35205600	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:35190200-35212000	Weak transcription	Brain Angular Gyrus	brain
12	chr6:35191200-35212000	Weak transcription	Primary T cells from cord blood	blood
13	chr6:35191400-35226000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:35192200-35211400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:35194000-35209400	Weak transcription	Thymus	Thymus
16	chr6:35194000-35225600	Weak transcription	Primary B cells from cord blood	blood
17	chr6:35195600-35210600	Weak transcription	Spleen	Spleen
18	chr6:35197000-35205600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:35199200-35211800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:35199200-35212200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:35199400-35208800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:35199400-35209200	Weak transcription	Adipose Nuclei	Adipose
23	chr6:35199400-35211800	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:35199400-35212000	Weak transcription	Brain Anterior Caudate	brain
25	chr6:35199400-35216200	Weak transcription	Brain Substantia Nigra	brain
26	chr6:35199600-35204000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:35199600-35205400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:35199600-35209800	Weak transcription	Gastric	stomach
29	chr6:35199600-35210400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:35199600-35211200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr6:35199600-35215600	Weak transcription	Hela-S3	cervix
32	chr6:35199600-35226600	Weak transcription	Esophagus	oesophagus
33	chr6:35199800-35205600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:35199800-35205600	Weak transcription	Right Atrium	heart
35	chr6:35199800-35205600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr6:35199800-35206200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:35199800-35206800	Weak transcription	Ovary	ovary
38	chr6:35199800-35212200	Weak transcription	HepG2	liver
39	chr6:35199800-35226200	Weak transcription	Pancreas	Pancrea
40	chr6:35200000-35204200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:35200000-35206000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:35200200-35204000	Weak transcription	Left Ventricle	heart
43	chr6:35200400-35205400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:35200400-35205600	Strong transcription	Osteobl	bone
45	chr6:35200600-35225000	Weak transcription	Fetal Brain Male	brain
46	chr6:35201200-35205800	Strong transcription	Aorta	Aorta
47	chr6:35201400-35226200	Weak transcription	Stomach Mucosa	stomach
48	chr6:35201600-35211800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr6:35201800-35205400	Weak transcription	Right Ventricle	heart
50	chr6:35202000-35204400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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