Variant report

Variant	rs4709704
Chromosome Location	chr6:163758941-163758942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163743568..163746151-chr6:163758711..163760918,2	K562	blood:
2	chr6:163757980..163760301-chr6:163766336..163768728,2	K562	blood:
3	chr6:163751984..163754408-chr6:163756474..163759819,3	K562	blood:
4	chr6:163755571..163762023-chr6:163831891..163837157,6	MCF-7	breast:
5	chr6:163757896..163760585-chr6:163774528..163776997,2	MCF-7	breast:
6	chr6:163751446..163754906-chr6:163755143..163760328,4	K562	blood:

Variant related genes	Relation type
ENSG00000270419	Chromatin interaction
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10945892	0.86[JPT][hapmap]
rs11759068	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11964527	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12662804	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12663140	0.91[ASN][1000 genomes]
rs12664344	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3734284	0.94[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4709705	0.91[EUR][1000 genomes]
rs4709706	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4709707	0.88[CEU][hapmap];0.83[CHB][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4709708	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4709709	0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56654356	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62428053	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62428054	0.80[ASN][1000 genomes]
rs62430070	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62430071	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62430072	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62430073	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62430074	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6932137	0.83[CHB][hapmap]
rs6932471	0.81[CHB][hapmap]
rs742331	0.84[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs882246	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1022610	chr6:163591786-163814041	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv605188	chr6:163697439-163772096	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4709704	MAP3K4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163745200-163767000	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr6:163745600-163773600	Enhancers	Brain Substantia Nigra	brain
3	chr6:163746600-163759400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:163746600-163759800	Enhancers	Brain Anterior Caudate	brain
5	chr6:163746600-163759800	Enhancers	Brain Hippocampus Middle	brain
6	chr6:163746600-163764400	Enhancers	Brain Cingulate Gyrus	brain
7	chr6:163751600-163759200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:163751600-163759400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:163753600-163759000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:163754200-163760000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:163754400-163760400	Enhancers	Fetal Muscle Trunk	muscle
12	chr6:163754600-163760200	Enhancers	Left Ventricle	heart
13	chr6:163754600-163760800	Enhancers	Fetal Muscle Leg	muscle
14	chr6:163755000-163760200	Enhancers	Lung	lung
15	chr6:163755400-163759800	Enhancers	Brain Angular Gyrus	brain
16	chr6:163755800-163759400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:163756200-163759800	Weak transcription	Fetal Kidney	kidney
18	chr6:163756400-163759000	Weak transcription	Esophagus	oesophagus
19	chr6:163756800-163759800	Weak transcription	NHDF-Ad	bronchial
20	chr6:163756800-163759800	Weak transcription	Osteobl	bone
21	chr6:163756800-163764800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:163757000-163759600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:163757200-163759400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:163757200-163759800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:163757200-163759800	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:163757200-163759800	Weak transcription	Fetal Thymus	thymus
27	chr6:163757400-163759000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:163757400-163759600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:163757400-163759800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:163757400-163762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:163757600-163759000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:163757600-163759000	Enhancers	Fetal Heart	heart
33	chr6:163757600-163759000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr6:163757600-163759800	Weak transcription	Fetal Lung	lung
35	chr6:163757800-163759200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:163757800-163759600	Weak transcription	Placenta	Placenta
37	chr6:163757800-163760000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:163758000-163759000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:163758000-163759000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:163758000-163759400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:163758000-163759400	Weak transcription	HUVEC	blood vessel
42	chr6:163758000-163764200	Weak transcription	Spleen	Spleen
43	chr6:163758200-163759000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:163758200-163759800	Weak transcription	Right Atrium	heart
45	chr6:163758200-163760000	Weak transcription	Adipose Nuclei	Adipose
46	chr6:163758800-163760200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:163758800-163760200	Enhancers	Psoas Muscle	Psoas
48	chr6:163758800-163760200	Enhancers	Right Ventricle	heart
49	chr6:163758800-163760200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr6:163758800-163762600	Enhancers	HSMMtube	muscle

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